Are you taking the bar off?
I have had Ernie Ball MusicMan Axis and EVH guitars, and the EBMM cases were built so as to allow the guitars to be put away with the bar in place - which was a bit of an oddity, as the Gotoh version of the Floyd Rose they use has the easiest pop-in/pop-out bar arrangement of all I have owned...
The Peavey Wolfgang, Gibson Les Paul and Fender Strat (whether MIA, MIJ or MIM), when equipped with a Floyd Rose, all require you to remove the bar before putting the guitar away in the case. All of those have the typical Floyd Rose bar, with the screw-on/screw-off collar on the bar. If you try to close the cases of any of those with the bar still in place, there is contact and pressure on the bridge (and for some, the case won't even close completely).
Although I have had a few PRSs, I never had one with a Floyd Rose, so I can't say for certain...but I would imagine the bar has to be removed before storing the guitar in the case., similar to those I have noted above.
John
thegrumpyoldman