Yes, I would say that you have an electrical problem!
Both engines should be separated by the engine harness/hull harness/helm locations. Meaning that the Port engine battery bank should power the Port helm instruments, and the Stbd engine battery bank should power the Stbd helm.
On many boats up to 30 feet or so, the Stbd engine harness/hull harness will include your HLBB (house load battery bank) of which powers the main cabin needs, Nav Gear, etc. when selected.
Even when sharing a Port side cranking bank, the harnesses should still separate these engines, instruments, key switches, etc.
Some owners/mechanics will disconnect batteries for the winter. When these are reconnected upon re-commissioning, often a Negative cable is forgotten.
If nothing else has been changed, you may want to begin by tracing all of your cables down.
Make sure that each battery bank makes it's own independant "system negative common" connection to each engine.
IOW, Do NOT share Negative connections between battery banks. We want redundancy here!
By chance do you have an OEM wiring schematic.... and if so, has any of this been changed from OEM?
Can you post photos of it?
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