Keeping alignment on multi-sided machining is one of the harder things to get right and can be really frustrating to learn. I did a lot of sanding to flatten out < 0.5mm offsets in two sided cuts early on.
This thread has some good examples of how people do it (enl_public has some strong workholding fu)
Many of the folks who seem to get it right put locating pins into the stock before the first op and then use those to locate the part when inverting, that or a machined jig which holds the part in each orientation. Otherwise you are relying on your measurement of the part width (and height) agreeing exactly with the machine’s measurement to get the workpiece zero in the correct place for the second op if you’re measuring off, say, the bottom left corner. There’s a few posts about this in the gallery
Try not to re-zero for the workpiece whenever possible as that’s a source of possible error, most of the good workpiece manipulation tricks work by cancelling out errors.
The locating pins trick works because they get drilled into the stock at whatever the machine thinks that distance should be so, as long as you don’t mess with the machine between cuts, those distances match up when you flip the part.
I’m slowly switching to using the spoilboard as my zero instead of the top of the stock and learning to use an edge finder properly to zero in places the C3D block can’t do, like lower right corner.