Best guess, the wrong buffer in play, the B/C is not coming back far enough, and the catch is only catching the bottom of the carrier; not raising up in front of the bolt isntead.
Pull all the way back on the charging handle, and the face of the bolt should stop about 1/4" to 1/8" in front of the back of the ejection port, but behind the bolt catch. Also, on the last inch'ish of the pull, the charging hand tension should be about the same as from half way back (and not harder instead the last inch)
If you have the correct buffer and recoil spring length in play and the above it correct, then next shotgun the upper open, and insert a empty mag. The follower should raise the bolt catch all the way up, and if this is not happening (catch not binding in it receiver slot and the problem at hand), then you may have to pull the bolt catch to check the catch spring channel for debris that you may have missed when the catch spring and buffer was installed).
Lastly, what stock on the rifle, since if you have an A-1 or after market stock that uses a butt stock screw, could be that the butt stock screw it too long, and now protruding into the back of the receiver tube to block the buffer from coming all the way back isntead.