I have heard of engines containing systems, sometimes a system contains multiple engines and sometimes there are engines composed of subengines and systems and so on. So it seems they are used interchangeably. Although I believe sometimes they are used to differentiate between different levels of scope. Meaning that for example it may be defined within bounds of a specific project that engine may contain multiple systems, but no other engines. I have no idea if there is a general rule or recommendation about it.
Edit: Come to think about it I believe engines tend to refer to real-time systems.