And after giving constantinople it reset all buildings to level one, so my run is basiclly destroyed, I could play on but if I always lose my economy power and even the buildings get downgraded that isn't lots of fun. Seperate from this why get the building even dowgraded, maybe I don't understand the constantinople mechanics behind that but it doesn't feel good.

First of all respect for playing independent hunters if you are new to the mod. They are a challenge. Secondly, it might be a bug or it might be related to your game rules setting. In the game rules you can choose how many super imortant and special cities a player is allowed to own. I suggest that you select "unlimited". Rome and Constantinople are metro areas or whatever and if you are unlucky your setting it at "none". Playing Akritai early on with certain settings is a first class ticket on the pain train.

Do you know what happens if you go over this special citie cap? I like to play independent hunters because it's one of the hardest challenges you can get in ck3 but haven't read the game rules that are special to this mod, so I will try to find out if it was a problem of the game rules or a bug.

Independent hunters are indeed very hard. If you want to there is also an option in the game rules setting that makes it even more difficult. You can start the game as a count with a nasty curse.
In your case it looks to me you accidentally signed up for even more challenges via the game rules setting.
Maybe start a game as a ruler (Camilla f.e.) who controls one of the major cities from the start of the game and see what happens. Most def check your current settings.

Most of the settings are fair in the sense that if you set domain limit to +3, then everyone can have three additional domains. If you set conversion speed to max, then your enemies can convert their conquests really quickly too. If you max out sickness and pestilence, then everybody has a big problem.
The setting with the major cities screws players only, it would seem.

I looked at the description with the major cities and it says only constantinople and rome and I only controlled rome, so maybe it was just a bug, maybe I could try to report it and sending my gamefile.

Yeah, then it might just be a bug.