I think it is not strictly related to heavy fighting/population. It happens also in low population times. Like all three factions have one bar and it happens. High population makes it more frequent but it might be some backend bug.
This happens with full servers. It happens also when you went in Cyrodiil in a delve and want to get out again. You can just try it until it works.
In IC there is an actual bug, though:
When you are in upper IC and want to go down to the sewers, usually you would be protected after the loading screen. I noticed recently I wasn't getting any protection anymore after going down into the sewers. I gather it is connected to long loading screens, as if you were already using up the duration of the protection while you were in the loading screen.
For the love of all that is holy I really wish they would add a quest board to pick up all district daily quest once without having to go up and down 6 times.