Can you see it?
Two unterminated (red) conductors.
Yes, but the photo is not centered on those. Secondary.
Are you looking for a breaker hold down?
The one used by Square D is not visible from the angle of the photos. You would need to look from the left side and below the 100 amp breaker.
Would it be the bent hot bus bar and/or connection with the ground/neutral bus bar?
Here’s that view. That’s part of the concern. I’ve got another photo which shows the issue right away but the first two have enough to identify it also.
The grounded bus looks cocked. Is it loose?
Then you must be asking about the breakers being cocked on the mounting rail.
That’s more evidence. 
I didn’t jiggle them, but those are both more evidence of what was done.
Here’s the give away photo.
The 100 amp breaker was on the right side. Now the cover has been cut to allow the breaker to be moved to the left side.
As you mentioned about the breaker hold down, I couldn’t see one on the new 100 amp main and the original on the right was cut off. Everything in the panel looked crooked, especially the main disconnect.
The owner(older lady) said a linesman for the power company in his off time had “installed a new panel for me about 6 years ago”.
I don’t know if this mod is allowed but with all the cockeyed parts, I referred it to an electrician. Whoever did this was not all that concerned with craftsmanship and I wonder what he did to the bus connections behind the main.
Nice!
I also see a white conductor being used for other than a grounded conductor that has not been permanently relabeled. There is also a grounded conductor double lugged with a grounding conductor. But these aren’t nearly as interesting as your main find.
back fed breaker not secured