Oh yah! Definetely mixed signals.

But this is on th Jam page:

Q: Can I edit my game once I submit?

You can fix game breaking bugs in your submission and upload those. If your game is unpleasant or unplayable due to technical issues, we want you to fix those! You just cant add new features or gameplay. or things like that.

The part about the game being "unpleasant or unplayable" was my best guide. And also, "You just cant add new features or gameplay. or things like that." is pretty clear.

I tried to get clarification on certain issues we had with really bad balance in our game because it just got boring if you made it past the 4 wave because it didn't get any more difficult. Never heard back so we made the judgement call to go ahead with the fix.