New York City FC might be comfortable at Yankee Stadium, but their uncertain status regarding a permanent home created a scheduling conflict which forced the team to relocate one of its final two home matches out of state. The worst part — it could happen again.

NYCFC, who play in Colorado on Saturday night, will play their home match against the Houston Dynamo on Sept. 23 at UConn’s football stadium in East Hartford, Conn., some 110 miles away from Yankee Stadium, because a Yankees makeup game booted them out of The Bronx. Yankee Stadium requires 72 hours to transition between soccer and baseball, and with NYCFC just tenants at the ballpark, the boot wasn’t all that surprising.

MLS Commissioner Don Garber told The Post that Yankee Stadium has been “great” for where NYCFC are today and credited NYCFC and Yankees for their terrific partnership.

“I think, you know, when you’re launching a new team nothing is perfect,” Garber said at NYCFC House, the team’s pop-up shop in the Meatpacking District. “But we wouldn’t be where we are today if it wasn’t for the relationship with the Yankees.”

When asked if the league still envisions NYCFC’s potential stadium in the five boroughs, Garber responded with a sharp “yes.”

But where exactly NYCFC are in their stadium search is anyone’s guess. The club remains optimistic and has looked at dozens of sites within the five boroughs, with a pit stop at the Belmont Park site in Elmont, L.I., a possible solution outside the New York City limits.

Proposals to develop the land must be submitted by Sept. 28. The Islanders also are expected to submit a proposal for a new arena at Belmont.

NYCFC president Jon Patricof, appearing on the “Soccer in the City” podcast earlier this week, said the team brought over the Chief Infrastructure Officer from parent club Manchester City to work full-time in New York City on the stadium search.

Patricof also revealed that NYCFC have come close on “many potential sites” but pulled out of one at the last minute.

“Right now we have multiple sites under active consideration — some involve public processes and some are private,” Patricof said. “I think this is going well and we’re as far along in terms of progress certainly since I’ve been here over the last 18 months.”

The scheduling conflict doesn’t mean it’s sped up the process.

“It doesn’t change anything we’re doing with a stadium, but there is a change in my need to talk more actively about it,” Patricof said. “I have known since day one that I took this position that one of the big things that might happen is this — a home game moved.”

If NYCFC reach the MLS playoffs, other potential conflicts could arise. The Yankees could reach the postseason, but more certain, Rutgers will play a football game against Maryland at the Stadium on Nov. 4, just a day before NYCFC could host a home playoff match Nov. 5.