Git stash not applying all my changes

Git stash not applying all my changes

I am working on a group project. I made a bunch of changes to my files and
right before I pushed to gitHub I noticed there had been a new update so I
ran the commands
git add .
git commit -m "some message"
git stash
then I updated with github
git pull
I changed a gem file and two other places that called for the gem
'rmagick' because it causes me issues.
Then I ran the command
git stash pop
It asked me to commit the changed files and I did,
I ran the git stash pop again but not all of my updates came back. Please
help me so I do not lose 3 hours work.
When I run git stash show -p I can see all of my changes! I think ....