Try something like this:
montage file1.jpg file2.jpg -geometry +0+0 -background none output.jpg
This will make the border between images as small as possible and whatever is there will be transparent.
To see a demo of the difference using builtin images, try these and compare:
$ montage rose: -resize 100x60 rose: -geometry +0+0 -background none montage.jpg
$ display montage.jpg &
$ montage rose: -resize 100x60 rose: montage.jpg
$ display montage.jpg &
See Montage Usage.
If you post an example of what you're getting and manually edit together an example of what you'd like as a result, we might be able to get a little closer to that.
Here are examples that I like better than the ones I originally posted above:
montage \( rose: -resize 100x46\! \) rose: -background gray montage.jpg
montage \( rose: -resize 100x46\! \) rose: -geometry +0+0 -background none montage.jpg
