If you build a portal over a chunk boundary, it can become bugged and some portal blocks will no longer be there. The remaining portal blocks work normally and updating them will delete them. It seems to be caused by reloading the area by crossing from the overworld to the nether whether you're going through an overworld portal that would connect to the bugged portal or a nearby portal. This has happened to me with two different portals and both times the nether side portal was broken. If you try to go to the nether from a portal that links to a would be bugged portal, it takes you to a different nearby portal instead. A portal breaking like this might not happen the first or second time the area is reloaded, but once it does break, it'll keep breaking fairly consistently.