diff --git a/src/cmd/go/internal/load/pkg.go b/src/cmd/go/internal/load/pkg.go
index 153399d83e6..3c7cd44ee33 100644
--- a/src/cmd/go/internal/load/pkg.go
+++ b/src/cmd/go/internal/load/pkg.go
@@ -87,6 +87,7 @@ type PackagePublic struct {
 	CgoFiles          []string `json:",omitempty"` // .go source files that import "C"
 	CompiledGoFiles   []string `json:",omitempty"` // .go output from running cgo on CgoFiles
 	IgnoredGoFiles    []string `json:",omitempty"` // .go source files ignored due to build constraints
+	InvalidGoFiles    []string `json:",omitempty"` // .go source files with detected problems (parse error, wrong package name, and so on)
 	IgnoredOtherFiles []string `json:",omitempty"` // non-.go source files ignored due to build constraints
 	CFiles            []string `json:",omitempty"` // .c source files
 	CXXFiles          []string `json:",omitempty"` // .cc, .cpp and .cxx source files
@@ -144,6 +145,7 @@ func (p *Package) AllFiles() []string {
 		p.CgoFiles,
 		// no p.CompiledGoFiles, because they are from GoFiles or generated by us
 		p.IgnoredGoFiles,
+		// no p.InvalidGoFiles, because they are from GoFiles
 		p.IgnoredOtherFiles,
 		p.CFiles,
 		p.CXXFiles,
@@ -371,6 +373,7 @@ func (p *Package) copyBuild(opts PackageOpts, pp *build.Package) {
 	p.GoFiles = pp.GoFiles
 	p.CgoFiles = pp.CgoFiles
 	p.IgnoredGoFiles = pp.IgnoredGoFiles
+	p.InvalidGoFiles = pp.InvalidGoFiles
 	p.IgnoredOtherFiles = pp.IgnoredOtherFiles
 	p.CFiles = pp.CFiles
 	p.CXXFiles = pp.CXXFiles
@@ -2493,7 +2496,7 @@ func PackagesAndErrors(ctx context.Context, opts PackageOpts, patterns []string)
 	}
 
 	if opts.MainOnly {
-		pkgs = mainPackagesOnly(pkgs, patterns)
+		pkgs = mainPackagesOnly(pkgs, matches)
 	}
 
 	// Now that CmdlinePkg is set correctly,
@@ -2547,50 +2550,63 @@ func CheckPackageErrors(pkgs []*Package) {
 // mainPackagesOnly filters out non-main packages matched only by arguments
 // containing "..." and returns the remaining main packages.
 //
+// Packages with missing, invalid, or ambiguous names may be treated as
+// possibly-main packages.
+//
 // mainPackagesOnly sets a non-main package's Error field and returns it if it
 // is named by a literal argument.
 //
 // mainPackagesOnly prints warnings for non-literal arguments that only match
 // non-main packages.
-func mainPackagesOnly(pkgs []*Package, patterns []string) []*Package {
-	matchers := make([]func(string) bool, len(patterns))
-	for i, p := range patterns {
-		if strings.Contains(p, "...") {
-			matchers[i] = search.MatchPattern(p)
+func mainPackagesOnly(pkgs []*Package, matches []*search.Match) []*Package {
+	treatAsMain := map[string]bool{}
+	for _, m := range matches {
+		if m.IsLiteral() {
+			for _, path := range m.Pkgs {
+				treatAsMain[path] = true
+			}
 		}
 	}
 
-	matchedPkgs := make([]*Package, 0, len(pkgs))
-	mainCount := make([]int, len(patterns))
-	nonMainCount := make([]int, len(patterns))
+	var mains []*Package
 	for _, pkg := range pkgs {
-		if pkg.Name == "main" || (pkg.Incomplete && pkg.Name == "") {
-			matchedPkgs = append(matchedPkgs, pkg)
-			for i := range patterns {
-				if matchers[i] != nil && matchers[i](pkg.ImportPath) {
-					mainCount[i]++
-				}
-			}
-		} else {
-			for i := range patterns {
-				if matchers[i] == nil && patterns[i] == pkg.ImportPath {
-					if pkg.Error == nil {
-						pkg.Error = &PackageError{Err: &mainPackageError{importPath: pkg.ImportPath}}
-					}
-					matchedPkgs = append(matchedPkgs, pkg)
-				} else if matchers[i] != nil && matchers[i](pkg.ImportPath) {
-					nonMainCount[i]++
-				}
-			}
+		if pkg.Name == "main" {
+			treatAsMain[pkg.ImportPath] = true
+			mains = append(mains, pkg)
+			continue
 		}
-	}
-	for i, p := range patterns {
-		if matchers[i] != nil && mainCount[i] == 0 && nonMainCount[i] > 0 {
-			fmt.Fprintf(os.Stderr, "go: warning: %q matched no main packages\n", p)
+
+		if len(pkg.InvalidGoFiles) > 0 { // TODO(#45999): && pkg.Name == "", but currently go/build sets pkg.Name arbitrarily if it is ambiguous.
+			// The package has (or may have) conflicting names, and we can't easily
+			// tell whether one of them is "main". So assume that it could be, and
+			// report an error for the package.
+			treatAsMain[pkg.ImportPath] = true
+		}
+		if treatAsMain[pkg.ImportPath] {
+			if pkg.Error == nil {
+				pkg.Error = &PackageError{Err: &mainPackageError{importPath: pkg.ImportPath}}
+			}
+			mains = append(mains, pkg)
 		}
 	}
 
-	return matchedPkgs
+	for _, m := range matches {
+		if m.IsLiteral() || len(m.Pkgs) == 0 {
+			continue
+		}
+		foundMain := false
+		for _, path := range m.Pkgs {
+			if treatAsMain[path] {
+				foundMain = true
+				break
+			}
+		}
+		if !foundMain {
+			fmt.Fprintf(os.Stderr, "go: warning: %q matched only non-main packages\n", m.Pattern())
+		}
+	}
+
+	return mains
 }
 
 type mainPackageError struct {
diff --git a/src/cmd/go/testdata/script/mod_install_pkg_version.txt b/src/cmd/go/testdata/script/mod_install_pkg_version.txt
index 2c14ef737b3..fd02392af1b 100644
--- a/src/cmd/go/testdata/script/mod_install_pkg_version.txt
+++ b/src/cmd/go/testdata/script/mod_install_pkg_version.txt
@@ -143,7 +143,7 @@ stderr '^go: warning: "example.com/cmd/nomatch\.\.\." matched no packages$'
 
 # If a wildcard matches only non-main packges, we should see a different warning.
 go install example.com/cmd/err...@v1.0.0
-stderr '^go: warning: "example.com/cmd/err\.\.\." matched no main packages$'
+stderr '^go: warning: "example.com/cmd/err\.\.\." matched only non-main packages$'
 
 
 # 'go install pkg@version' should report errors if the module contains
diff --git a/src/cmd/go/testdata/script/mod_run_nonmain.txt b/src/cmd/go/testdata/script/mod_run_nonmain.txt
new file mode 100644
index 00000000000..036755d2d1a
--- /dev/null
+++ b/src/cmd/go/testdata/script/mod_run_nonmain.txt
@@ -0,0 +1,18 @@
+! go run $PWD
+! stderr 'no packages loaded'
+stderr '^package example.net/nonmain is not a main package$'
+
+! go run .
+stderr '^package example.net/nonmain is not a main package$'
+
+! go run ./...
+stderr '^go: warning: "\./\.\.\." matched only non-main packages$'
+stderr '^go run: no packages loaded from \./\.\.\.$'
+
+-- go.mod --
+module example.net/nonmain
+
+go 1.17
+-- nonmain.go --
+// Package nonmain is not a main package.
+package nonmain
diff --git a/src/cmd/go/testdata/script/mod_run_pkgerror.txt b/src/cmd/go/testdata/script/mod_run_pkgerror.txt
index fd7060aaa86..48f900dd346 100644
--- a/src/cmd/go/testdata/script/mod_run_pkgerror.txt
+++ b/src/cmd/go/testdata/script/mod_run_pkgerror.txt
@@ -1,12 +1,26 @@
+# https://golang.org/issue/39986: files reported as invalid by go/build should
+# be listed in InvalidGoFiles.
+
+go list -e -f '{{.Incomplete}}{{"\n"}}{{.Error}}{{"\n"}}{{.InvalidGoFiles}}{{"\n"}}' .
+stdout '^true\nfound packages m \(m\.go\) and main \(main\.go\) in '$PWD'\n\[main.go\]\n'
+
+
 # https://golang.org/issue/45827: 'go run .' should report the same package
-# errors as 'go build'.
+# errors as 'go build' and 'go list'.
 
 ! go build
 stderr '^found packages m \(m\.go\) and main \(main\.go\) in '$PWD'$'
 
+! go list .
+stderr '^found packages m \(m\.go\) and main \(main\.go\) in '$PWD'$'
+
 ! go run .
-	# TODO(#45827): This error should match the above.
-stderr '^go run: no packages loaded from \.$'
+! stderr 'no packages loaded'
+stderr '^found packages m \(m\.go\) and main \(main\.go\) in '$PWD'$'
+
+! go run ./...
+! stderr 'no packages loaded'
+stderr '^found packages m \(m\.go\) and main \(main\.go\) in '$PWD'$'
 
 -- go.mod --
 module m