I noticed on several occasions that Space Engine seems to place Io and Europa incorrectly in their orbital positions. For example, at this time both of those moons should be occulted by Jupiter, but Space Engine shows them in very different positions withing their orbits.
I didn't check too many other moons of Jupiter. You can compare against many position calculators online or another program like Celestia. I searched but did not see this mentioned. Is this a known bug?
This is not a bug, but restriction of current version. SE uses simple Keplerian orbits for planets. This is relatively precise for major planets, but very unprecise for moons. Proffesional astronomical software uses complex numerical models like vsop87 to compute precise positions of the Solar system bodies. This is on my TODO list.