Whenever I make a new character, the areas around Klapeida (West/East Siauliai Woods, Miners Village) are bugged and the map says 100% complete although in the adventure journal it is not (0%).
I tried changing the maps and relogging but it still shows map 100%. I can’t explore the map.
How to solve this? 
You need to complete Tenet Chapel Main quest line to get Seal of Space, and use it in the stone close to Klaipeda Entrance (a small corridor before getting there) to access the secret area.
Did you climbed the carts by the mine entrance? On the right side.
Also there is another side on the map that have some side quests and a Stats Point Statue