I also can confirm that timwarp occasionally becomes incontrollable while in space in 1.11.1. Switching back to KSC and back to the spacecraft makes it controllable again.
Never have i seen this bug in earlier versions of the game.
Also I noted that Kerbal Alarm 3.13.0 clock has become buggy with this version of the game. Sometimes it doesnt let me add alarms or overwrites existing alarms with new ones. Maybe there is a link since both functions deal with time?