Portal room (more importantly, end portal blocks) can get overridden by other structures such as mineshafts, ancient cities, and also the new trial chambers.
Step to Reproduce:
Load up a world with the seed given and go to the coordinates.
Trial Chambers Overrides Stronghold:
Seed: 940028760242419482
Coordinates: 1443 -17 -1505
Ancient City Overrides Stronghold:
Seed: -3307142256062781398
Coordinates: 786 -44 809
Expected Result:
Stronghold would replace the structure, rather than the structure replacing the stronghold
Observed Result:
The stronghold (and the end portal blocks) get replaced by said structure and you can't enter the end.
Linked issues
is duplicated by 2
Attachments
Comments 8

The issue with mineshafts is tracked at MCPE-155092. The same issue with geodes has been fixed (MCPE-129861).
There was also an issue regarding fossils intersecting end portals, however that has been resolved as Incomplete due to a lack of updated seed + coordinates: MCPE-40017.
Bug Fix in more detail:
The stronghold should generate only after all other structures in the game and features have been generated.