Just feel free to ask if you need any other information about the setup and configuration
A picture maybe, because your post is less than clear. For instance,
Hi, I have 3 Xbee s2c modules with me and 3 Arduino M0 for each of them.
Three Arduinos for each XBee means 9 Arduinos, which I doubt is what you have.
I can't imagine why you have some XBees in API mode and some in AT mode. They should all be in the same mode.
The Arduinos are running some code which is missing from your post.