Stop over / stop by can suggest your visit will be short or that you’ll visit on the way to something else. ‘Drop by’ is another term which is often used this way too. Example: On my way to school, I’m going to stop over to pick up that book I forgot at your house. Come over is more literal and straightforward. It doesn’t suggest anything other than the fact that a person will arrive somewhere. Example: I can come over after school today.

I’ve never heard anyone say “stop over” “Stop by” is normally used and is generally used to mean the same thing as come over. Stop by my house on your way back from the store. Come over to my house after you go to the store.

they are almost the same in that can be used interchangeably. stop over = more American - actually visit and stay for a while. come over = more British and perhaps denoting a visti that might be vey brief. I have a feeling that the difference is more between US and GB than any real difference.

Stop by means that the person will only visit for a very short time "I'll stop by to give you the baked cookies." Come by means the person will stay there for a longer period of time "I will come by to help you on your project."

A stop over is the same as "staying overnight" it has a length of time added to a come over, i.e you will be coming over but not leaving, stopping in the place you are visitng, if you say I'm stopping by or passing by, meaning, so I'll take the opportunity to see you, it has a limited time i.e you'll visit someone on the way to do something else or see someone else . A come over is just a visit to see someone. " I'll come over to see you later" " Can iIcome over now' etc.