Allen, who had been considered a leading contender for the MVP award, appeared to be in pain towards the end of the game as he grabbed his right elbow.
It seemed to have stemmed from Allen being sacked by Jets rusher Bryce Hall in one of the last plays of the game at MetLife Stadium.
Afterwards, however, Allen was fairly relaxed about his condition even if he acknowledged he did receive a knock.
"There's some slight pain," he said. "I'll get through it."
Generally, though, Allen's demeanour in the post-game press conference was by no means upbeat.
Defeat saw the Bills lose two games in a row after beginning the season with six wins on the bounce, and Allen's own performance came under intense scrutiny.
It has even been suggested his display was poor enough to take him out of the MVP running after the 26-year-old was 18-of-34 for 205 yards – a season low – and two interceptions.
Allen was also sacked five times, and he seemingly believed responsibility for the defeat was on him.
"It's tough to win in this league when you're playing a good team and your quarterback plays like s***.
"[I] made some bad decisions tonight that really hurt our team. [There's] a lot to learn from, lot to grow from.
"But that's not the standard we hold ourselves to, that's not the ball we play. Lots to look at, lots to learn from."
The 6-2 Bills remain top of the AFC East despite the defeat and will hope to avoid a third consecutive loss when they face the Minnesota Vikings on Sunday.