Here's a reproduction test case where a macro super unit is used twice in the same flow.
1) attach a flow machine to an empty gameobject
2) make a macro superunit and attach it in the same flow.
3) provide two different gameobject inputs to the two superunit instances.
In my simple testing, it seems to happen when a gameobject is the input, fine when int.
As can be seen in the second image, all connections work correctly except for the one leading to Output.
Disconnecting the second instance from the flow immediately reverts the first output to its correct output.
(edit: also not the Manual Event, forgot to replace, but was initially happening onMouseDown)
The Flow Graph:
In the (first) Super Unit: "Test 2"
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