Today I caught several pokemon without any problem. Then I encountered a bagon (lucky me) and tried to capture it. My pokeballs failed and got the message that my pokebank was full. I clearly had like 8-9 full slots left. I don't know if it happens to other players atleast it did to me. Also I deposited some pokemon from my party to the box and had no issue with this at all.

Just a suggestion - but I know alot of content is dependent on registering when you re-log. The Blue server has had some great up-time today in comparison to the days prior; so I must ask if you have re-logged since then? Perhaps it has yet to read that you released a few.

I was able to catch alot of pokemon last night which went into bank. I came back this morning and 2 were depositted into the bank. just this bagon wouldnt get inside (havent tested the next pokemon just party slot > bank worked fine)

I had this problem too before. Turns out even if you have free slots in your 60th PC page, the system will count the Pokemon you have in party as though they were also stored in PC. So basically you can get up to 60 max PC pages minus however many Pokemon you're carrying in party.