Hey John,
I say cut them out. In the past I've occasionally let oversights like that go so I could just get on with the build... and every time after the model was finished I regretted it. We are our own severest critics; every time I look at these models my eye goes right to the irritating flaw!
I'd go after them carefully with the point of a new No. 11 X-acto. Any little slips will be camouflaged by the new photoetch ladders on the bulkheads and hidden by wood deck below. Best of all, once you've done it you can enjoy your build and never give those #$&%#@! stairs another thought!