With 27.1 I have many of these issues. Recently, after some of these problems, I searched and found a link between two node tags in xml, pointing to an input pin of another subpatch, but this pin was regularly linked in the subpatch xml code.
Usually copy/pasting would solve this; but I had to modify the xml, since that buggy link, as evidence, had never got lost during copy\paste operation.
Also, after xml surgery, another strange behavior disapperead: when saving a subpatch in the patch containing buggy link, this subpatch was then docked inside itself, 2 identical patches docked together - useless to alt-3 just one cause both would be affected and deleterious have been ctrl-W in just one, since this would delete subpatch.
It’s recent stuff, and should be somewhere; if it’s of any interest I’ll post here - but we’re running towards 27.2, sooo…