At the end of Bad Timing (2003) when Aeryn and John were transformed into crystals, their pulse pistols are clearly visible in the pile (the pistols had not turned into crystals). However, when they were reconstituted at the beginning of 'The Peacekeeper Wars' the first thing they did was pull their guns which were, supposedly, still in their holsters.
The piece of crystallized organic material that is Aeryn and Crichton's baby, which stayed inside Rygel, has never gone thought the decrystallizing machine. Nevertheless it started growing, and Rygel's stomach acids did not harm it, but it was established earlier in Farscape (1999) the series that Rygel's stomach acids are not the same fashion as others, which could mean it could be conducive to not only restoring the baby crystal, but nurturing it as well. Alternately, the energy emitted from the decrystallizing machine might have radiated into the room, affecting and restoring the crystal in Rygel's stomach.
After Moya enters Starburst, Chiana and Stark greet an Eidelon. Instead of any Starburst glow like Warp Drive, there are stars outside indicating they are not in Starburst.
In "Bad Timing", the Eidelons have a Raspy Voice and their Outer Eyes along with Inner Eyes were moving. In the movie, the Outer Eyes are held shut and they all do not have Raspy Voices.
The audio for the miniseries is pitched lower and makes all characters have different sounding voices to the series because they filmed it at a slightly faster frame-rate than normal broadcast speed.