I think the shows have actually fielded this issue rather well. Temporal investigations was the start, then the timecops in Voyager and SNW. The Trek timeline is in a constant state of flux to the point that the TOS bridge and the SNW bridge are supposed to be the same place, and the fact that time travel is so easy is a great explanation for how everything in the ‘past’ and future keeps changing on the whims of producers at Paramount.