What version of Go are you using (go version)?

$ go version
go version go1.12beta1 darwin/amd64

Does this issue reproduce with the latest release?

Yes the issue is reproducible with the latest version of go (go1.12beta1)

What operating system and processor architecture are you using (go env)?

$ go env
GOARCH="amd64"
GOBIN=""
GOCACHE="/Users/subhash_sharma/Library/Caches/go-build"
GOEXE=""
GOFLAGS=""
GOHOSTARCH="amd64"
GOHOSTOS="darwin"
GOOS="darwin"
GOPATH="/Users/subhash_sharma/go"
GOPROXY=""
GORACE=""
GOROOT="/Users/subhash_sharma/.goversions/go1.12beta1"
GOTMPDIR=""
GOTOOLDIR="/Users/subhash_sharma/.goversions/go1.12beta1/pkg/tool/darwin_amd64"
GCCGO="gccgo"
CC="clang"
CXX="clang++"
CGO_ENABLED="1"
GOMOD="/Users/subhash_sharma/subash/go.mod"
CGO_CFLAGS="-g -O2"
CGO_CPPFLAGS=""
CGO_CXXFLAGS="-g -O2"
CGO_FFLAGS="-g -O2"
CGO_LDFLAGS="-g -O2"
PKG_CONFIG="pkg-config"
GOGCCFLAGS="-fPIC -m64 -pthread -fno-caret-diagnostics -Qunused-arguments -fmessage-length=0 -fdebug-prefix-map=/var/folders/w0/d6l19r7j3dbg7fq56_nn4l340000gp/T/go-build083506298=/tmp/go-build -gno-record-
gcc-switches -fno-common"

What did you do?

The following testscript reproduces the issue:

# listbug.txt

# prime the mod cache with a replaced module
go mod download example.com/fruit@v1.0.0
go mod download

go list ./gopath/pkg/mod/example.com/replacedfruit@v1.0.0
! go list ./gopath/pkg/mod/example.com/fruit@v1.0.0

-- go.mod --
module mod

require example.com/fruit v1.0.0

replace example.com/fruit => example.com/replacedfruit v1.0.0

-- main.go --
package main

import (
    "fmt"
)

func main() {
    fmt.Println(fruit.Apple)
}

# mod/example.com_fruit_v1.0.0.txt

-- .mod --
module example.com/fruit

-- .info --
{"Version":"v1.0.0","Time":"2018-10-22T18:45:39Z"}

-- go.mod --
module example.com/fruit

-- fruit.go --
package fruit

const Apple = "apple"

# mod/example.com_replacedfruit_v1.0.0.txt

-- .mod --
module example.com/fruit

-- .info --
{"Version":"v1.0.0","Time":"2018-10-22T18:45:39Z"}

-- go.mod --
module example.com/fruit

-- fruit.go --
package fruit

const Apple = "apple"

What did you see?

go list ./gopath/pkg/mod/example.com/fruit@v1.0.0 passes with output

example.com/fruit

go list ./gopath/pkg/mod/example.com/replacedfruit@v1.0.0 fails with output

 go: directory gopath/pkg/mod/example.com/replacedfruit@v1.0.0 outside available modules

What did you expect to see?

go list ./gopath/pkg/mod/example.com/replacedfruit@v1.0.0 should pass because that is the directory in which the replaced example.com/fruit is now located

go list ./gopath/pkg/mod/example.com/fruit@v1.0.0 should fail because that module is now located elsewhere due to the aforementioned replace in go.mod.

cc @bcmills @myitcv