The Present - S3-E9
Continuity mistake: When The Flash reveals to Julian that he's Barry, he pulls back his cowl, leaving it around his neck. But in shots of Barry's back after Julian says his sister died, the cowl is gone. The cowl is around his neck in all the other shots.
Attack on Central City - S3-E14
Factual error: Wells states that there are "precisely 90,000" possible 5-digit combinations for the keypad (to abort the nuclear code). However, there are actually 100,000 possible combinations (10^5).
Continuity mistake: When Barry and Kara get shot outside the bar, at first the spot of blood on Barry's shirt is bigger than when Iris and Mon-El later get to the scene. (00:34:00)
Continuity mistake: Near the end when Iris and Joe are talking, Iris sits with her elbow on the couch and her head against her hand. In the next shot, her forearm is resting on the couch, and her hand is hanging down, away from her head.
Continuity mistake: The explanation that Cisco draws about the endless cycle changes in between shots, not counting the added words "past", present", and "future" (which he could have written when off camera, not that it would make sense to do so since he already explained what was past, present, and future). Where the loop crosses itself is higher up as well as the "FF + TR" being different.
Revealing mistake: When Iris is sitting in bed recording the message for Barry, she is holding her iPhone so that the start button is on the left side, but the "video record" button appears on the right. Additionally, her right hand covers the speaker area of the phone fully, including the front facing camera. It is impossible for Iris to be recording the video live and reveals that the video footage was recorded ahead of time. The illusion that the video is being recorded by Iris live is further ruined by the fact that the room lighting is turned off in the scene, but the recording is well lit. (00:02:55)