Following the fix for #ZBX-12893 I now get this updating my system:

Calculating upgrade... Done
The following packages will be upgraded:
zabbix-agent zabbix-frontend-php zabbix-get zabbix-proxy-mysql zabbix-server-mysql
5 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade.
Need to get 4,174 kB of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-server-mysql amd64 1:3.2.9-2+xenial [1,634 kB]
Err:1 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-server-mysql amd64 1:3.2.9-2+xenial
Hash Sum mismatch
Get:2 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-agent amd64 1:3.2.9-2+xenial [159 kB]
Err:2 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-agent amd64 1:3.2.9-2+xenial
Hash Sum mismatch
Get:3 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-frontend-php all 1:3.2.9-2+xenial [1,876 kB]
Ign:3 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main i386 zabbix-frontend-php all 1:3.2.9-2+xenial
Get:4 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-get amd64 1:3.2.9-2+xenial [59.4 kB]
Err:4 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-get amd64 1:3.2.9-2+xenial
Hash Sum mismatch
Get:5 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-proxy-mysql amd64 1:3.2.9-2+xenial [446 kB]
Err:5 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main amd64 zabbix-proxy-mysql amd64 1:3.2.9-2+xenial
Writing more data than expected (446576 > 445578) [IP: 127.0.0.1 3142]
Get:3 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main i386 zabbix-frontend-php all 1:3.2.9-2+xenial [1,876 kB]
Err:3 http://repo.zabbix.com/zabbix/3.2/ubuntu xenial/main i386 zabbix-frontend-php all 1:3.2.9-2+xenial
Hash Sum mismatch
Fetched 5,602 kB in 0s (15.4 MB/s)
E: Failed to fetch http://repo.zabbix.com/zabbix/3.2/ubuntu/pool/main/z/zabbix/zabbix-server-mysql_3.2.9-2+xenial_amd64.deb Hash Sum mismatch

E: Failed to fetch http://repo.zabbix.com/zabbix/3.2/ubuntu/pool/main/z/zabbix/zabbix-agent_3.2.9-2+xenial_amd64.deb Hash Sum mismatch

E: Failed to fetch http://repo.zabbix.com/zabbix/3.2/ubuntu/pool/main/z/zabbix/zabbix-frontend-php_3.2.9-2+xenial_all.deb Hash Sum mismatch

E: Failed to fetch http://repo.zabbix.com/zabbix/3.2/ubuntu/pool/main/z/zabbix/zabbix-get_3.2.9-2+xenial_amd64.deb Hash Sum mismatch

E: Failed to fetch http://repo.zabbix.com/zabbix/3.2/ubuntu/pool/main/z/zabbix/zabbix-proxy-mysql_3.2.9-2+xenial_amd64.deb Writing more data than expected (446576 > 445578) [IP: 127.0.0.1 3142]

E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?