Mechanic cut my fender liners - should I be upset?
 

I recently had to take my 2010 Pathfinder to a muffler shop recommended by my general repair shop.
They replaced my blocked cats, and removed the rear cat. I picked the vehicle up and drove to a nearby town, about 100 miles. The SES light came on a little while after getting under way, and there was a rattle, similar to the one I had asked them to fix.
When I got back, I took it to the shop and told them what I saw. They kept the car for a day or so ,and when I picked it up the shop owner said they had forgotten to tighten the 02 sensors, and that was the cause of both issues; rattle and SES light.
Fast forward to last weekend. I need to replace the orig equipment struts and rear shock so I by started putting penetrating oil on all the bolts now. When I looked behind the tires I see that my fender liners look different and I can see wires I don't remember. I just replaced the crank shaft sensor a few months ago so I had just taken the fender liner off of the passenger side.
I feel like this is something I should have been consulted about before they cut into my vehicle. It's only 7 screws, if I remember correctly, and I noticed one of those was missing.
Should I approach the shop about this? Do I need to explicitly say every time I go to a shop that I need to be called before any physical alterations are performed?

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area removed by mechanic in red