Weird issues in 10.0.3

First off yes I know there are updates for FCPX but this problem is at my local college where I have no control over updates.
I was asked to help a student (not my own) with problems with her project.
She was getting weird black frames in parts of her Primary Story-line and at times it was intermittent during playback.
However at Share Export it was there.
First I thought its the h.264 footage shes clinging too but after a Transcode still there.
When I went into the Project window I did notice the weirdest thing.
She has audio clips in the Primary but its clearly Video in the timeline. No Connected Clips other than other audio (foley).
I selected the audio clip and deleted which reveals the actual video.
Prior to that I selected the audio and did a reveal in browser and noticed it was originally a clip but she only needed the audio.
the only fix (quick one since it was due that evening)was to:
select audio in primary
reveal in browser
delete audio clips from primary
insert to primary with audio off

this seemed to have fixed the problem with the black frames.
however for the life of me I cant replicate how the audio got embedded in the Primary without deleting the original video.
Ive searched the man pages, personal notes and even online tutorials.
I either missed a step or I need to re-learn FCPX again.

I don't have access to her project/events so I cant fiddle with it anymore.
It was a favor to the college for helping her but now I'm really curios.