'Tiny flies' are most likely fungus gnats. They like wet and organic conditions- and unless that is resolved, they will be around. I doubt very much they came from outdoors (unless it is very wet around where they were kept? - like a soggy area). You didn't say how long semps were in that plastic container - soil probably styed wet and heaven for fungus gnats. Why are you growing semps indoors? You mentioned outdoors, so it would be best for the to be there and stay there year round. They are very hardy. They are also etiolated, which means they are not getting enough light. Best if you take them outdoors and slowly acclimatize to proper sunlight (otherwise they will get sunburn). They can be grown in ground or containers, but suffer if indoors.

It is hard to tell what are bugs on Aeonium; could be mealy bugs - but there would be also a white, cotton-like mass (almost like a web) if that's what they are. Could be some mites (?) or even aphids. Can't see them...try spraying with rubbing alcohol to reach everywhere. Keep out of sunlight while spraying with anything. They would also benefit from outdoors - better light, better air circulation - but watch for sunburn.

You didn't say where you are (why don't you add that info to your name???) - temps could make difference...

Interesting, thank you! I'm in New York, USA. I think I will plant them outside now, knowing how hardy they are. I've had them for about a month and they came in some SUPER moist soil and I wasn't able to re-pot it until a week after. Once I re-potted it is when the flies started coming. I also noticed there were some dead plants hidden underneath which probably didn't help the issue. They have only been in the plastic container for a couple days while I was swapping out plants and waiting for a new pot to come.

I will take your advice on the aeonium and spray it to see if that helps.