It sounds like network connections may be timing out so that either the incoming connections are not made or time out before being completed or the exports have a similar problem, perhaps because the target database is not available at that moment?
The cause? Well, network set up is one possibility if users are, quite reasonably, restricted to the amount of network resource they can use at any one time. If they are it will likely have been set for a generous value for interactive work but maybe not so generous for the way that batch files can crunch data. If the batch is parallel processing (rather than serially processing the lines) some other effect may be in play but the result is the same.
Alternatively it could be a no-data to report situation giving no update for export - but I'm guessing you have porbably already covered that.
What to do ....?
You could consider putting some control statements into the batch file to slow it down a little and see if that improves things. And of course check with your network people to see if they can predict a reason.
Or you could consider creating a more sophisticated batch program using, for example, VB and building in error checking and reporting.
And I suppose ultimately there is always the Data Pump option where such needs are catered for on an 'industrial' scale.
I don't consider myself at all expert in those areas so have little to offer by way of practical guidance but hopefully others will be along shortly to help.