The Movie particularly suffered from pacing issues, and from being placed as far forward in the timeline as it was. Fluttershy especially could’ve been captured in Canterlot, and absolutely nothing would’ve changed, for how few lines she had, and in fact it would’ve been cool if she’d managed to befriend multiple guards just from being nice to them, offscreen.
It also didn’t help that Twilight’s spell variety was seriously limited; Cadance was the only one to use a shield spell (or really, the only alicorn to act half-competently in that siege, because she didn’t know it wouldn’t work), and no one teleported when they logically can, to escape.
Shadow Play hardly pretended the problem couldn’t be solved in some way, just the right way to go about it. I think the latter had less logical holes in that regard.