I think it's possible sound and music resources don't work well yet.
Sounds added to the Sound folder don't show up in the dropdown as resources when making an action to play it.
I noticed that in .99.2 earlier today, and in .99.3 it's the same thing. That may be why .caps made in 98.9 or prior are failing in .99.2 and above.
(FAKE EDIT: Seems this is confirmed, Candescence was having trouble saving his .cap, and after removing the sounds from the Sound folder he was able to save his .cap without any problems.)
Also, there seems to be something up with collisions. See CharmyBee's Ghost Shooter clone here. Start the .cap and walk down towards the bottom edge of the layout, avoiding all "monsters." The player's health will begin to deplete even when not touching a monster, so either there are objects that aren't rendering or there is something up with collisions.
(REAL EDIT: Actually, it might just be the .cap. I haven't found any evidence elsewhere that collisions are messed up.)