Matsatsantsa were left silenced by the Absa Premiership basement dwellers at Mbombela Stadium this past weekend as Bakgaga pipped a 1-0 victory to end United's chance to set a new PSL record of going 20 league games unbeaten.
Baxter is currently engaged with SAFA over his potential return as head coach of Bafana Bafana after SuperSport confirmed last week they have allowed the former Kaizer Chiefs coach to speak with South African football's governing body.
And, within just days of that announcement, Matsatsantsa found themselves on the losing end in the league for the first time since the opening day of the season, and while Baxter felt his side were lacking in several departments on the day, he also admitted talk of his potential departure may have negatively affected the team.
"My situation with SAFA might be the reason why SuperSport lost to Baroka FC in this past weekend's league match," the club coach revealed.
"It's very possible. I think everybody has found it a little difficult and it's something that you can suspect without making any excuse," reveals Baxter.
"I wouldn't like the players to walk up the field after losing and just forget the fact that our quality was poor, organisation was poor and our individual and team technique was poor.
"That is probably why we lost the game, but in the back of their minds I'm sure they were wondering what was happening [with Baxter's future]."
The Brit is also unsure if the 2-0 Nedbank Cup last-16 win against third-tier side KwaDukuza United is enough to hail a return of complete concentration to the players.
"We know what our [South African] cup games are like, we know that they are not easy. We are trying to rotate our teams so we are not losing that continuity, and maybe it [the uncertainty surrounding Baxter] is in the back of their minds, so there's a lot of things, lots of things [that can affect the team].
"It's difficult for me to answer specifically and say, ' ja, it's surely that' but I think it was a mixture of things, but we are through [to the quarter-finals].
"We scored two goals and we could've scored more. If the quality wasn't what I wanted in terms of organisation and technique... I think it's Nedbank Cup [which is full of surprises] and we are in the next round, so I'll take it."
Matsatsantsa have a heavy fixture list piling up in April, with the Nedbank Cup holders also away to Barrack Young Controllers of Liberia in the CAF Confederation Cup first-leg playoff on Sunday at Antoinette Tubman Stadium in Monrovia.