I changed the Absolute tolerance from 0,001 mm to 0,01 mm, but the issue is still present with fillets less than 1 mm. 
However, when I changed it again to 0,1 mm, the fillet was fine.
I rebuilt the surfaces in this particular area while temporarily changing the Absolute tolerance to 0,0001 mm to split them more accurately. Then I reverted to 0,001 mm tolerance and joined them to the main model. Now the fillets work as usual.
Charging port door BUG 2.3dm (194.9 KB)
I figured out that with 0,001 mm tolerance Rhino would still split the surfaces in a slightly wrong way and once the surfaces are joined together, there is an extremely small deviation where the 3 surface edges meet together in a T-shaped joint. In the past I wrote requests several times in different topics to use 10 times smaller tolerance only for the “Trim” and “Split” commands, while the rest commands should use the Absolute tolerance. That way, many issues like the one I mentioned here would not occur at all. I did a quick search and just found two samples of my request to have a more precise trim/split setting: