We use scrum, and have daily stand-ups, sprint plannings and other meetings over conference calls.
That is the 1st problem. Conference calls especially large one tend to be met with silence. This is across the board. We have the same problem but you can make some strides to change this.
What's a good way to ask this without feeling like I'm challenging them?
One tactic we use at my work is to ask direct questions to individual instead of asking a question to everyone. The way we do this is by letting it be known we plan to ask everyone at the end of the call/meeting if they have any thoughts or questions and what action items they took away from this. We call it our "Round Table".
This serves 2 goals. One is to make sure people are taking some kind of notes as they will be ask what is their take away or action items at the end of the meeting and two people will be more prepared with questions or information at the end.
This works very well for us and we have a very large company and meet with many people over many different cultures and this still works well. I would give that a shot. Maybe bring the idea to management.
Typically we end our meetings like this:
"Ok so starting from the left, Sara what have you got... Ok thanks Sara. Bob what have you got... Ok thanks Bob. Jan what about you... Oh you are having an issue with such and such well Bob is working on a similar issue and he has some resources you might not. Get with Bob after the meeting to see if you can help each other. "
This has be very good at including everyone without feeling like we are targeting a specific person and it serves as good clarification without others having to feel "dumb" for asking so they don't have to stay silent.
Personally I do not understand the need to stay silent. I don't care what others think if I ask a question. I have a job to do and if I don't know something I need to know. Does not matter to me if someone thinks its a dumb question. For me I just need the info so I can do my job well.