You should test all the equipment shortly before the meeting (but with enough time to fix things if there are problems).
If you start a meeting knowing the systems are unreliable, you can ask everyone to go on mute except when they need to talk - this is good practice even if the system is working properly (especially in larger meetings). Also ask anyone who can to wear headphones to minimise audio feedback.
If the problem is limited to one or two callers, you could ask them to leave the conference and arrange for them to be briefed/consulted once the meeting is over. However, you would need to defer any decisions/action points requiring their input until you've spoken to them.
If things deteriorate to a level where you can't have an effective meeting you should either try a different phone system or postpone the meeting until after any problems can be fixed.