Scotch Bonnets, Capsicum chinense, can’t cross with bells, C. annuum. Cross pollination cannot affect the current year’s fruit/pod quality. That is determined solely by the “mother plant”, regardless of pollination. What can get affected is the genetic contents of the seeds; i.e. if one plants the seeds, hybrids can appear.
If the bells were hot, it’s because the seeds that were planted were outcrossed (with Hot Wax, or other C. annuum), or one of the hot bell-types got mixed in the seed packing facility.
I do a lot of pepper breeding and experimenting. There is a lot of confusion in the marketplace these days, both by misnaming and mild lookalikes of hot varieties. If one gets seeds from Southern Exposure Seed Exchange, they’re pretty good at selling the real thing. Choose Jalapeño “Early” or “M” for hot ones. Usually, the early type is a bit hotter and is often just sold as “Jalapeño”. It’s a smaller type, which develops crack-like patterns as the pods ripen . In stores, it’s a gamble what you get.
Small bees can create random hybrids, but only within certain limitations. Of the three main cultivated varieties, here’s the general consensus:
•Capsicum annuum crosses with C. annuum, not C. chinense or C. baccatum
•C. chinense can cross with C. baccatum, e.g.: CxB; this creates what’s called a “genetic bridge”. What’s useful for pepper breeding is to first make this hybrid, because now one can introduce CxB traits into C. annuum. In other words:
•C. annuum can cross with CxB, e.g.: AxCxB
This is keeping it simple, because there are a bunch of other Capsicum species, with different hybrid potentials.