Comment 9 for bug 807303

I can reproduce this message by adding many https repositories to sources.list. For example, with these sources (which are public, so you can try this yourself):

deb https://debathena.mit.edu/apt precise debathena
deb-src https://debathena.mit.edu/apt precise debathena
deb https://debathena.mit.edu/apt quantal debathena
deb-src https://debathena.mit.edu/apt quantal debathena
deb https://debathena.mit.edu/apt raring debathena
deb-src https://debathena.mit.edu/apt raring debathena
deb https://debathena.mit.edu/apt saucy debathena
deb-src https://debathena.mit.edu/apt saucy debathena
deb https://debathena.mit.edu/apt trusty debathena
deb-src https://debathena.mit.edu/apt trusty debathena
deb https://debathena.mit.edu/apt utopic debathena
deb-src https://debathena.mit.edu/apt utopic debathena
deb https://debathena.mit.edu/apt vivid debathena
deb-src https://debathena.mit.edu/apt vivid debathena

I get:

$ sudo rm /var/lib/apt/lists/debathena*
$ sudo apt-get update
…
W: Size of file /var/lib/apt/lists/partial/debathena.mit.edu_apt_dists_quantal_debathena_source_Sources.bz2 is not what the server reported 31194 16209
W: Size of file /var/lib/apt/lists/partial/debathena.mit.edu_apt_dists_saucy_debathena_source_Sources.bz2 is not what the server reported 31029 24393
W: Size of file /var/lib/apt/lists/partial/debathena.mit.edu_apt_dists_trusty_debathena_source_Sources.bz2 is not what the server reported 26334 16209
W: Size of file /var/lib/apt/lists/partial/debathena.mit.edu_apt_dists_utopic_debathena_source_Sources.bz2 is not what the server reported 26237 16209
W: Size of file /var/lib/apt/lists/partial/debathena.mit.edu_apt_dists_vivid_debathena_source_Sources.bz2 is not what the server reported 14 251

This does not happen with the same repositories over plain http.