How hard can it be to lop them off and re-touch the crater?
Half my locomotives have green class jewels. I put as many markers as I can on my models. An AC-11 can have four markers and two class lamps. Mine get them all! Yet I insist on 2-rail track, and a scale that makes the track scale out to 4'8 1/2" gauge. Takes all kinds.
Cut those offending suckers off, fill the hole with JB Weld, and touch up with a black paint marker.