Could be the delay time as mentioned. If it is a larger system and you are scanning other larger systems at the time, once the scanner moves on to the other systems it can take a while to return.
It could also be something as simple as human error on their part. It takes a second or two for a repeater system to pick up the mic output and repeat it. If talkers press the PTT (push to talk) button and immediately start talking then the first second or two of their transmission can get cut off. The entire transmission can get cut off if it was very short, like "10-4" only.
Another issue might be with how you scan. If set up to scan only selected IDs then the non-selected IDs won't be scanned. That is good if you purposely want to not scan certain IDs due to lack of interest in them. If set up to scan/search for any ID then you will get everything on that system, a lot of which might not be of interest to you.
And of course it could be the way they set up their system. Some system have issues and even they cannot hear each other consistently! We have a few of those in the DFW area, especially on the P25 systems. I hear a lot of them asking for a repeat or just saying I heard only garbled noise. And as someone else mentioned, the simulcast systems can be notoriously riddled with issues.