Since you have a response from the engineer, I guess it doesn't really matter but I am still confused about the original issue. You said the trench was dug to the proper depth? They ran short of concrete so you only got 6" of depth yet it appears the top of the footing is level? I don't get how that happens. Is there a step in the footing we can't see.
My second thought is that the engineer's response is a bit odd. Are you going to remove the blocks and just add more concrete to the top of the footing? If that's the case, I'd just rip it out and build it properly.
I also question the original design/construction. You said this is a retaining wall, correct? How much earth is it supporting? A retaining wall's ability to resist overturning depends on the weight of the soils 'holding down' the footing and the connection from the wall to the footing. That footing looks awful meager for this purpose.
Finally, make sure you have good drainage to minimize the weight of the soil you are holding back. Good luck with the rest of your project.
Yeah, something isn't adding up to me either.
Inspector says footing depth was 'correct'. To me, that means that the bottom of the footing 'hole' was deep enough from the top edge of the form that the correct/desired depth of concrete could be poured/placed into said footing form.
But the top surface of that footing is flat and level. And gravity means that when the concrete was put into said form, it went to the bottom of the 'hole' first and then was filled up to the top edge of the form.
But there is only ~6" of concrete there.
When you run out of concrete, you don't 'fill' the form all the way to the top. Which means that you wouldn't have a flat and level 'filled' form full of concrete.
And how the heck are you going to get the 12" thick concrete when you already have the top surface of the concrete footings at the correct elevation?

Dig underneath the footing, magically clean off the bottom of the footing, and somehow pour concrete underneath the existing too thin footing?
It kind of sounds like the engineer told you how to fix the footing if it were poured not wide enough.
It sure sounds like the contractor really needs to remove the mispoured zone, re-excavate and re-form the area, get reinspected, and THEN pour the footing correctly. With the clean-up and bonding agent to 'connect' the re-poured concrete to the existing concrete. All while maintaining the rebar connections throughout the footings.
I think the engineers need to actually do a site visit and inspection and then come up with a way to fix the contractor's screw-up, not just tell you a 'fix' based on a picture or two and a phone call.
And absolutely do NOT accept the contractor trying to say that "It's fine". Plans said 12" thick concrete, he only put in 6" thick concrete. Not even close.