It isn't a timeline flub. They've always maintained that the episode content and story content alternate in sequence. They've never said the timeline was 1:1 with the real world.
Shows pad their timelines like this all the time to keep the show going at relatively real time taken in the long term (this is to account for character aging/real life events impacting the timeline). Some dump timeskips between seasons, some like to end their seasons on cliffhangers that pick up almost immediately after with the new season so they build up their spare time with midseason timeskips or dump a timeskip after the first episode of each season. Some do midseason breaks and have timeskips there. Keeping to a normal timeline isn't as important for series not set in the present, but many shows do it anyway or use a floating timeline.
Incidentally, this is why holiday episodes tend to be funky/not canon.
Anyway, for Defiance, just consider the episode/mission sequence to be canon with the exact length of time between/during each to be variable (episodes last longer than an hour, missions last longer/shorter than a week).
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