Most likely due to the 2 minute quarters. The same thing would happen playing short quarters in Dynasty on NCAA 10.
Speaking of minor glitches though, whenever the defense jumps offsides they glitch through the line completely. As in, they teleport about 3 yards behind my o-line and THEN do the jump offside animation from NCAA 10.
That and also every time the referee is shown (when calling/describing a penalty) the camera is halfway underground.