Ex-Borg Riley says she was assimilated at Wolf 359 (re: The Best of Both Worlds: Part 2 (1990)). The Borg ship that battled Federation forces at Wolf 359 later went to Earth and was ultimately destroyed by actions of the Enterprise-D, which would mean that none of the newly-assimilated Borg could have been transported back to the Delta Quadrant. (The fifth season episode Infinite Regress (1998) provides another instance where a character - one of Seven of Nine's personalities - claims to have been assimilated at Wolf 359, thus making the same continuity mistake.)
When Riley leaves the room where Chakotay is recuperating, she passes through a heavy door, outside of which can be glimpsed a computer wall panel. When Chakotay sneaks out of his room later, the wall panel is within his room, he just has to get to it without being seen. The door blocking his way (as well as the wall the doorway was embedded in) is no longer there.
After Chakotay has a vision of Riley's childhood memories, he tells Riley that he saw her favourite flower: bluebonnets. Riley confirms that she used to pick them back home in Texas with her grandfather. But the flowers shown in the vision are not American bluebonnets, they are English bluebells, a completely different species of plant.
The seam on Riley's skull cap makeup is visible when she isn't wearing her wig.
When Chakotay links with the group, he has visions of memories, including some from Riley. One of the images is of Riley playing with her grandfather from a third person's point of view. Riley's memories should be from her point of view.
During the autopsy scene of the Borg drone, it can be seen still breathing in the final shot of the scene.
When Chakotay's unconscious body is being dragged away from the scene of the firefight, his left leg can be seen kicking himself along to aid the actor pulling him.