Are we using nfl tie breaker rules when deciding final playoff spots?

For the most part, yes. There are a few that are incredibly complicated when you get too far that are not included.

Yeah, I was questioning on MFN-2 as a team with a losing conference record qualified over a team with a winning conference record. I know my team shouldnt have got the spot but I thought the team that had same conference record as my team should have since they did beat me during regular season.

I haven't gone through the tiebreakers in MFN-2 (I did see the situation) but one rule is that once a team has been eliminated the tiebreakers start again between the remaining teams. When you get 4 teams all in a tiebreaker it starts to get difficult to do by hand.

That said, it's not outside of the realm of possibility that there's a flaw in the algorithm. I'll make a note to look closely at this situation when I get a chance to make sure that there's no error that needs to be fixed.