git subtree pull says that the working tree has modifications, but git status says it doesn't. What gives?

Question

If I do this in one of my repositories:

git subtree pull --prefix=frameworks/AquaticPrime --squash AquaticPrime

I get this:

Working tree has modifications.  Cannot add.

If I do this (in the same place, of course):

git status

I get this:

# On branch master
nothing to commit (working directory clean)

I'm not quite sure what's going on here. The git status command implies that I don't have modifications, so I'm assuming that the git subtree pull is referring to modifications in a different branch related to the subtree, but it's not entirely clear.

Can anyone provide enlightenment?