Szkoda - damage, detriment
Strata - loss
Szkoda czasu - Szkoda (czyjegoś) czasu - Damage (of somebody's) time
Strata czasu - (to) strata czasu - (it is) a loss of time
Meaning is similar, meaning it's time wasted, it's a waste of time, though I think using the first one implies more that it is someone's time that is being wasted, or is "damaged" - as in, not fully utilised - while the second is more passive, not necessarily referring to the subject per se, but being a more general lament - it's a waste of time, in general.
Observe & compare:
Szkoda całkowita = total loss (when referring to for example a car crash and the car is totalled)
Szkodnik = pest, lit. "damager"
Bilans strat i zysków = balance of losses & income
Stracić zaufanie (do kogoś) = to loose trust (in someone)