Marcin, yes I have the same issue in latter firmware. When making changes to the routes (as an example) and then applying, there is a delay between the time that the UCM indicates applying (with their spinning icon) and when the indication goes away implying complete and when the UCM will start to process incoming calls. The INVITE arrives, but the UCM does not respond and the caller just waits. Waiting a bit seems to sort it out.
In process calls are not impacted and I do not think outbound calling is although I cannot recall specifically testing for this. I notice is most when altering anything in the path of an inbound call that affects the answer.
I have gotten used to it so not much of an issue, but it can be an irritant when you think the configuration is complete and should be working only to test and then not have it work as you initially think something went awry, when it only needed added time.
While I have no real insight into it, only an observation, my opinion is that the apply indicator is not lock-step to the actual configuration update and reload that is need to employ the new settings and that possibly given the number and complexity of the changes or existing configuration, the time needed to recover to functional status may vary, so I may see the impact for a short period while other may see longer or shorter.
Just a guess though, but did scare me a little when I first came across it.