After further investigation into this I found out that this issue seems to arise on Conference Finals on both the Eastern & Western Conferences only in the playoffs.
After I managed to win and progress to the MLS Cup the home advantage seeding rules applied as it normally should for the Cup final.
I checked the Eastern Conference Final and it the match was played on a neutral stadium as well so it seems that this bug only occurs during the conference final stage of the playoffs
Not given Home advantage in MLS Playoffs despite being the 1st seed in conference.
in [U.S.A.] (Official) League Specific Issues
Posted
After further investigation into this I found out that this issue seems to arise on Conference Finals on both the Eastern & Western Conferences only in the playoffs.
After I managed to win and progress to the MLS Cup the home advantage seeding rules applied as it normally should for the Cup final.
I checked the Eastern Conference Final and it the match was played on a neutral stadium as well so it seems that this bug only occurs during the conference final stage of the playoffs