Very nice job on that Domino Squad episode! Some early notes from me:

Just before we go to the crawl, there is a fade to black which I think could use some retiming. As it is, it fades slowly and we get just a brief glimpse of El-Les before going completely dark. This feels off. I suggest either fading earlier or later.
Someone already suggested dropping that brief scene with Shaak Ti and Lama Su. I think it doesn’t really add too much and it might be better to keep the focus on the clones.
When the clones escape the base, the droids report four clones having escaped. However, when we next meet the group, only three are present. This should probably be addressed in some way.
The reunion scene with 99 could also use some trimming. Echo mentions the generals receiving word of an impending attack, which seems a bit odd considering they themselves witnessed the separatist fleet moving in. Not sure what the options here are, though.

These are all fairly minor nitpicks. I think you managed to craft the three episodes into a solid narrative.