Dr. Smith marches off from the Jupiter 2 to deal with the alien mirror, leaving Debbie the Bloop behind. When he arrives at the mirror, Debbie is there ahead of him and not out of breath.
When Smith breaks the mirror with a shovel, it's noticeably less reflective than before.
After John and Maureen enter the ship (shortly before Don shows John the cosmic radiation gauge), the outdoor noise does not attenuate until a good second after the door has closed.
The black wire used to pull over the table outside the Jupiter 2 during the cosmic storm at the beginning of the show is visible before the table "falls" over from the wind.
After Penny says "Mom's starting to fix lunch," she shouts "Mom!" However, this utterance does not match her actual lip movements at that moment.
When Penny is leading Debbie the Bloop to the mirror (right after Dr. Smith says "take that improbable bell ringer with you), a person is seen to the right of the mirror motioning, presumably to Debbie. They quickly duck out of view after a few seconds.