Yeah, agreed with Jason. This is likely an issue with your git server or the network traffic path between agent and repo server. It is possibly made worse by some semantics of your repository and the size of changes to fetch after the merges.
The repository may be too large and difficult for the server to pack to send to the client with your current network configuration.
Are these HTTP or SSH clones? Is your git server something like GitHub or something internally managed?
If your clones are HTTP AND you have an internal Git server AND there is some kind of reverse proxy in between agent and git server it might be that the reverse proxy is terminating the connection. Could be rate limiting, overload, excessive size of repo/changes to fetch. Similar for ssh clones if there are network load balancers in between your agents and the git server. If GitHub etc you should be able to google to find possible reasons they'd terminate connections.
If HTTP you can enable git debug env vars to see the specific errors curl is getting to try and narrow it down, e.g
export GIT_TRACE=1
export GIT_CURL_VERBOSE=1
There are similar flags for SSH clone debugging with a custom GIT_SSH_COMMAND, but won't go into that here.
-Chad