There are certain ways to remove unnecessary groups with only one objects in them, nut none of these are native.
One is a script: https://community.adobe.com/t5/illustrator-discussions/how-to-remove-redundant-groups-via-script/td-p/2548597
The other one is VectorFirstAid plugin: https://docs.astutegraphics.com/vectorfirstaid/vectorfirstaid-panel

Hi Egor --

I looked into what you said and did some digging on my own. The issue I have is that I have to use CADs that are quite old and worked on by other people, so there do tend to be things like empty layers and old groups with just a single object in them. This solution usually works for me now:

--Direct select one object and attempt to eyedropper.
--Doesn't work. I can assume the object is in a useless group.
--Hit "ungroup" command+shift+G once or twice. This should clear out the useless group
--Use eyedropper again and it typically works.

I hope this helps other people having the same problem. Thank you for all your thoughts on this! It was really annoying me.

I see what happens here, Robin.
Take a look at the video attached.
Study the file yourself, with both Layers and Appearance panels opened.

While these pants look very similar, the blue pair is different.
Grab the Group Selection tool (or Direct Selection, it doesn’t matter here), click both on their fills and locate both objects in Layers, using the dedicated button.
Notice each path is wrapped into a group (this is fine, but I hope you have a reason to).
Then, notice the circle marker for the blue pants group is not hollow — this means the group has a custom appearance applied.
Indeed, the Appearance panel shows it has a black stroke above the group’s contents... and a blue fill under the contents! And the contents — is the actual path with the same exact fill.

Now, when you click the right pants with the Group Selection, notice it’s the wrapper group gets the target on the circular marker, not the path inside. It means whatever appearance gets assigned manually or grabbed by the Eyedropper (if the settings tell it to — more on this later), it will be assigned to the group container — not the path.

Now pick the Eyedropper. Press Enter or double-click the tool’s icon to open the Eyedropper Options dialog.
I recommend to uncheck both Appearance options and never enable them until you get enough experience with the panel.
Now, make sure you target the actual path and not the group for the right pants (you can either click its appearance marker in Layers or double-click the Contents row in the Appearance panel to do this). When you click the black pants with the Eyedropper, the fill gets sampled properly — the fill, not the appearance, as the tool’s options now command.
So the blue pants are now black, but the group still have the 'custom' appearance, and its marker is full, not hollow. 'Custom' appearance can mean an effect applied, stroke and fill reordered, extra fill and stroke added — and this was the case for you. Target the group and click the Clear Appearance button to remove the extra stroke and the fill behind the contents of the group (it’s not visible anyway).

So how did it happen?
Let’s see (not recorded on video).
Deselect everything and don’t undo the steps above.
Grab Group Selection and click the blue (now black) pants. As mentioned before, since the group has only ONE object in it, the group gets targeted — not the only path in it.
Pick Eyedropper, open its Options and check both Appearance options back. This is what I believe you had set for it, right?
And now, if you now click the pants on the left, the tool will sample the appearance from the PATH, but will apply it to the GROUP — since this what is targeted in Layers, and since it’s because these are your settings for the tool!

So, again, this is very important to
1. Have groups only when you need them
2. Be dead sure on what’s targeted in Layers: targeting (circular marker) and selecting (square marker) are different states in Illustrator
3. Control your Eyedropper’s options and pick/apply appearance only when you control everything

Hope it helps.

I can't get the screen recording to post right now but I will work on that

Hi Egor -

Sorry for the delay. Here's an AI file and I am going to try to also post another screen recording so you understand what I am doing

Robin, if you still have the file (or have the same behavior again), would you mind isolating the top group it belongs to by removing other art (only for your privacy), and sharing the document here, for testing? I’d like to see if this is reproducible. Make sure it still happens with it. Thanks!

Egor--
I read your comment and have been experimenting with your suggestions. Checking / unchecking the Appearance options in the eye dropper tool does sometimes help, but it's very inconsistent. Just now I was having this issue again and the eyedropper wasn't working no matter how I had the appearance option configured. But I do thank you for your reply!

Robin, can you please check how the Appearance panel looks for this object selected (when not isolated and when it is) and what options do you have picked for the Eyedropper tool (specifically two Appearance ones at the top of the dialog).
Does the behavior change if you uncheck these options?