Continuity errors can happen when you edit ingredients, labware, or steps upstream.
You delete labware used in a transfer.
Step 1 fills wells used in Step 2. You delete Step 1.
One of your steps aspirates 7 uL from a well, but you change the well in deck setup to only have 3 uL.
Currently the Protocol Designer can’t address these for you. We can flag some steps that may have been affected by the upstream edits you made, but it’ll be up to you to fix them.