Hi,
this normally happens when you use a "horizontal mirror" on some optical part. When you attach more parts to it, either optical or functional, they get mirrored aswell. The mirrored engine there is only optical, BUT: you can place another real engine at the place where the hardpoint is, you just have to click into fake engine.You then have two engines at the same spot, one fake mirror engine and a real one.
Hope this helps