Poor microphones set up around the conference room that make it hard to hear everyone.
No webcam at all or a bad webcam setup that doesn't allow the remote attendees to see the gestures people make.
Multiple people talking at the same time, but having very quiet conversations.
Using a whiteboard, a projector or showing a screen by turning your computer around but not making it visible to remote attendees.
* Basically doing things that the remote people can't participate in.
Poor teleconference tool.
Low quality headphones/microphones.
Low quality or no web cams.
Process:
Failure to auto-mute attendees when they join meeting
Failure to actively manage mute during the meeting (some nitwit always starts eating potato chips).
Failure to ensure mics are well placed in conference rooms.
And I've found remotes to be better at intuitively following those rules than local employees. Because locals are face-to-face, there's no audio/video quirks, and misc noise (chewing, paper rustling) tends to be way less distracting.
EDIT - remotes also have a serviceable webcam on their laptop. Meeting rooms need good wide-angle cameras installed so the entire room of people can be broadcast. Employer issues decent Jabra headsets to all employees, so audio is covered - so again, it's a matter of installed good A/V in the conference rooms (particularly number and placement of mics).
Our current teleconferencing solution is "Zoom" and so far, it's been far better than previous software (primarily WebEx and odd combinations of 800 numbers). It allows default meeting settings (by corporate account and by user) and "mute incoming attendees" is checked on mine.
Another common (but not universal) rule is "cameras are ON". We want to see each other's faces while chatting remotely.
EDIT2 - good AV equipment isn't cheap. I asked about adding a Polycom system to one of our small "huddle" rooms and it was many thousands of dollars - not deal-breaking for a mid-size enterprise operation, but also not something any of us could fund on the spot. IT is slowly adding them to the smaller rooms as funds become available (all rooms that seat >4 were done when we moved into the space).