Deleted Messages still take space on iCloud When I logged into my iCloud account with Safari I saw, that backups on my iCloud take approx. 2GB: 

what was a bit strange for me because locally checking (ie. from system preferences -> iCloud), they take about half of that size: 



Then I looked up into other positions on the list and saw Messages take the rest of the 2GB I saw firstly:



It is strange for me, because as you can see in first image, there is no such position as Messages on the bar, only bigger Backup position. Then I deleted all the messages on my iPhone to see if anything changes, but it did not change anything in the size of messages shown in system preferences. I do not know if it is some kind of error, or messages will disappear from iCloud later.
You might have a backup from one of your old devices still saved in your iCloud account. From an iOS device, try to check by going to Settings>iCloud>Manage Storage>Backups. This page will list the backups and associated device with the backup. On my account, the total size matches the total size of the Backups listed in Safari.