Sometimes it's an issue with counting rests on the time signature. If they have eight measures of rest in 3/4 or 2/4 it's much different than 4/4. Explain everything in bite-size pieces. A simple concept that most beginners and some middle school students do not understand is that whole rests are the value of the measure in the current time signature. It could be 4 beats, 3 beats, or 2 beats.
For tempo issues with a metronome, break it down to quarter notes for one measure, then two, then four. Put eighth notes into that rhythm next with one measure, then two, then four.
We use rhythm bee and when I went from kids counting to playing the rhythm there was a huge realization of how many students can hide when counting. After understanding how to count with a met the rhythms we then play one of their first notes on that rhythm. It's no wonder they were struggling reading music when they can't play in time on a basic rhythm. It has improved considerably in the last few weeks just changing over to playing the rhythms. Sometimes students have disconnect because there is more going on when playing than just counting. I do a lot of hissing as well for articulations to clean them up.
Always ask questions such as 'Susie, who has the melody at measure 64?' Ask two or three students then you should explain what a melody is and why it's important to know where it is in the music.
I'm guilty of throwing too many things at students at once myself. Sure they can get through things but it's only 75-80% correct. Go back and work on those details/concepts. Many students have become professional in their ability to hide and not be heard/seen. Small groups to clean, small concepts to cover, and daily building. Don't move on to something new until they get those concepts you are working.