Sometimes the stacker tower shows "Extension blocked" but i can place it manually. sometimes it unstucks itself but sometimes it does not.

That looks like a very long stacker tower that's about to discover it still has room to dump before commanding the next extension, but isn't bothering to wait until it's verified that there isn't any before it starts displaying erroneous errors... I believe this issue on GitHub is referring to the same behavior: https://github.com/MaFi-Games/Captain-of-Industry-issues/issues/2590

Generally speaking, it will unstuck itself every time... unless the extension is actually blocked... but it can take, depending on length, anywhere from several seconds to theoretically minutes if you've managed to bounce off the 200-extension limit. I only ever got 60 deep before getting tired of the bad warnings, though.

My workaround is to only ever let them get 15-20 long before moving the main tower up (by deleting all but the final extension, then building the tower to match the remaining extension) and running the belts up to it. A couple of times, that has involved building a whole new station for the trains bringing it in, but at the moment, it's just a really long belt spanning the length of this massive station:

(You can see the moved stacker towers waiting for me to get around to stepping the belt up to the next row)

Correct, this happens with long rails due to how the scan\construction timings differ. It's on my TODO list.
Not an error per se but an annoying premature warning.

Fixed in the next patch.