While downloading large resource update on 5.3B4 and then again with 6.0 the downloads would work normally for a while (~3-20 minutes) and then stop and the downloads would repeatedly fail. Cancelling the download and restarting Logos would make the downloads start again for a while.
When this happened, LogosIndexer was not actually indexing or downloading, but the process consumed 2 CPU cores at 100%, from iStat you can see download traffic drop to 0 and the CPU usage ramp up:

I wondered if it was due to server load issues but this didn't seem to be the case (after restarting Logos many times and getting through the download at a snail's pace, I found the update URLs and downloaded them with a download manager without any problem)
Weird...
Edit:
I recovered the end of an indexer log from when it was failing:
5140.indexer-failing.log
Apparently the download jobs were timing out, but when I downloaded the files manually with an external download manager there were no hiccups at all...