Moving pistons sometimes don't get powered

This seems like the same behavior described in MC-11193, with the update order of the piston and slime blocks not being consistent across all activations.

Does MC-11193 describe your issue?

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I don't think MC-11193 describes my issue. (although I don't exactly understand the behavior they're showing)

From what I can see using /tick, the lower piston doesn't receive an update when the upper piston retracts after dropping the slime blocks and therefore doesn't extend. (as shown in the "duck" screenshot)
However when the block shown in the "duck" screenshot is removed (even if every other block that can be attached to the slime blocks is there) it does receive the update and extends as shown in the "duck2" screenshot.

From my understanding it works like this as long as the slime blocks never push the block shown in the "duck" screenshot, as placing it in the location it will end up in results in the piston being extended (however, placing it in between so it only gets pushed once still results in the piston not extending)

Could you attach a structure file to the issue so that I can also test it?

Assuming you mean ones from structure block then yes; I just did.

Here is my reasoning as to why this duplicates MC-11193:
When using /tick freeze and /tick step and copying the machine twice (running both at the same time), you can observe that on both contraptions, all redstone components move at the exact same time. Everything visually appears as though it should work the same for both, but it does not.

This is appears to be because when the piston is bud-powered by the observer above it, the piston which retracts over it is able to send a block update to the piston, and thus extend it. For whatever reason, adding blocks to the slime changes the block order, which seems to be what MC-11193 describes (a seemingly random and inconsistent update order with redstone components)

Since it's not super clear and MC-11193 is pretty broad, I went ahead and confirmed it. To test, just load the structure and pull the lever. The furthest piston will then be retracted, even though there's powered redstone pointing into it.