After Dr. Marr ramps up the frequency to destroy the Crystalline Entity, it starts to shake and resonate with the graviton pulses, but the star field behind the entity also shakes. Since the Crystalline Entity shakes but the Enterprise does not, the star field should not have shaken along with the entity; otherwise, the graviton pulses from the Enterprise would be proving themselves to be powerful enough to rattle the galaxy.
Just after the opening credits, as the crystalline entity turns up, three different people can be seen running away from certain doom - a young child (with Dr. Crusher) and two young adult blonde women - laughing as if they were having a great time. Given they were in mortal danger, it seems out of place.
When Data and Dr. Marr enter the turbo lift, and Data explains how the memories of the colonists have been transferred into his memory cells, Dr. Marr says, "Bridge." A few moments later when they arrive at the bridge and the turbo lift doors open, you can clearly see the same corridor they walked in from.
When Data and Dr. Marr arrive on the bridge as the Kallisko sends their distress call, the turbolift doors do not fully close and a sliver of the turbolift interior is visible. Several seconds later and before the scene cuts, the doors finally close.
Dr Marr threatens Data with dis-assembly if it's discovered that he has any involvement with the Crystalline Entity. Since it was already hashed out in The Measure of a Man (1989) that Data is a sentient being, her threat was not only empty, it should have been construed as her being unstable and dangerous. Data should have reported the matter to Captain Picard and the doctor should have been removed from the project.
Data is unable to stop the graviton beam that Dr. Marr initiated, explaining that she placed an access code on the system. Data has been shown to have great ability in creating and breaking elaborate passcodes. Dr. Marr should not have been able to put in place anything that he would not be able to crack, yet he is not even shown making an attempt.
While Picard and the bridge crew desperately search for a way to deactivate Dr. Marr's graviton beam, none of them suggest trying to move the ship. Moving the ship would change the aim of the beam, and putting distance between the Enterprise and the entity would lessen the effect on it. A ship as fast as the Enterprise could have been out of firing range in a matter of minutes, if not seconds.
At one point when Dr. Kila Marr scans the cave with Data, she holds the tricoder upside down.
Dr. Marr is aghast that Picard does not intend to fire on the entity on sight, believing it needs to be destroyed, not communicated with. She is fully aware that the entity is extraordinarily powerful and dangerous, able to lay waste to entire planets in a matter of hours. Firing on it without provocation could have easily led the entity to attack the Enterprise.