The number one thing that bothers me about Changeling is that they beam Nomad aboard.
For one thing, they believe Nomad is a space ship or probe. Would you beam a shuttlecraft on board? And Nomad had survived attack from their best weaponry; how does the the transporter suddenly have the power to disassemble it? If they could have disassembled Nomad, they should have done so during the battle.
For another, once you had disassembled that thing, why would you re-assemble it??? Send your transporter beam and disassemble Nomad – and boom, successful resolution to battle. Well done, captain. End of story.
I guess the rest of Changeling works ok, if you accept the premise that they had monumentally effed up by beaming that thing aboard, and now had to deal with the mistake. I might have no problem with the episode if Nomad came in via the shuttlecraft bay doors.