I'm running a local mirror for my university and I've met the same problem.
I thought it was hard disk problem so it took me about a week before I finally 
figure out the reason.
I did a lot of test, read through RSYNC logs and contacted with upstream mirror.
I've come to the conclusion that it was caused by filesystem error in the 
upstream.

The interesting point here is that:
RSYNC CANNOT FIX CORRUPTED FILES if they have the SAME TIMESTAMP and SIZE but 
are wrong in content.

There are at least two ways to fix this problem.
* Manually download the corrupted files (most of them are .bz2 index files in 
my case) through http.
  However, there's no way you can figure out how many files have been damaged 
before. 
* Use rsync --checksum option to fix the whole archive.
  But as far as I know most mirror sites refuse -c option because of cpu 
consumption.
  I managed to fix the problem by rsync -c with official archive.ubuntu.com.
  Be aware, connection may be closed if too many files are being compared with 
checksum,
  so I wrote a script to rsync smaller sub-folders in traversal way:
ubuntu/dists/devel
ubuntu/dists/devel-backports
...
ubuntu/pool/main/a
ubuntu/pool/main/b
...
ubuntu/pool/universe/a
ubuntu/pool/universe/b
...
ubuntu/pool/multiverse/a
ubuntu/pool/multiverse/b
...
ubuntu/pool/restricted
ubuntu/indices

Hope this may help for mirror sites.

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https://bugs.launchpad.net/bugs/1311652

Title:
  Error during update

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