git add adding ignored files

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You probably have a negative rule (include-again rule, the one that starts with an !) in your .gitignore file somewhere after the node_modules line.

git check-ignore has a bug/ambiguity in the docs. You expect that if git check-ignore node_modules/ prints node_modules/, then node_modules/ is ignored. But actually it prints a pathname if that pathname matches any ignore pattern – positive or negative. The only way to be sure is to use the -v (--verbose) option, which will make git check-ignore print the matching pattern.
Moreover, if git check-ignore -v says a directory is ignored, it doesn’t necessarily mean that all files in that directory are ignored. Example repo:

/
    .git/
    .gitignore
    node_modules/
        bar
        foo

$ cat .gitignore 
/node_modules/*
!/node_modules/foo

$ git check-ignore -v node_modules/
.gitignore:1:/node_modules/*    node_modules/
             ^ positive pattern => ignored

$ git check-ignore -v node_modules/foo
.gitignore:2:!/node_modules/foo node_modules/foo
             ^ negative pattern => not ignored

$ git add -A

$ git status
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#   new file:   node_modules/foo
#

So if git check-ignore -v node_modules/ says node_modules/ is ignored, do git add -A node_modules/ and then run git check-ignore -v --no-index against individual files that got added, to discover why they were added.

Update: I didn’t expect that: your .gitignore file is in “UTF-16 with BOM (byte order mark)” encoding:

$ cat .gitignore | hexdump -vC
00000000  ff fe 6e 00 6f 00 64 00  65 00 5f 00 6d 00 6f 00  |..n.o.d.e._.m.o.|
00000010  64 00 75 00 6c 00 65 00  73 00 0d 00 0a 00        |d.u.l.e.s.....|

That’s why git probably can’t handle it. Save the file in UTF-8 without BOM, that should fix the problem. But I also suggest filing a bug report against git check-ignore – in this corner case its output is clearly not consistent with what git actually ignores.

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