Not only was the other one in this hard to figure out, then it's thrown in again but with a past tense. Commmmeeee on. How are we supposed to learn these phrases...building blocks!
Since missing someone is more a state of being than an action, it's unlikely to be used in the progressive/continuous aspect. (I've been trying to think of natural examples, but I haven't found any so far. I've found some sing lyrics, but they seem strained.)
My understanding is that Falta here is the noun meaning Lack or Absence. So a literal translation of the sentence, though it doesn't make good English, would be "I felt your lack/absence", or in common English, "I missed you".