Ok Ok let me break it down here
First the tech side, this is an issue of HTTP/1.1 Virtual Hosting specs
Back in the day when they realized hey it doesn't make sense for all domains to have their own IP they changed the HTTP protocol to send a Host header that specifies exactly the name of the site that they want to connect to on a certain IP.
Now the only way to properly manage virtual hosting is via software, doing it by hand you'll go insane! Software is usually written 3rd party as its quite difficult to write in house, so there are a BUNCH of limitations.
Things that could have caused this problem, mannnn there's a bunch anything simple from rebuilding VirtualHosts (order is important) to maybe using alphabetical sorting, to even adding more IPs on the box and it having to re-organize previous entries could have caused sitetwo's vhost to appear above siteone's and that would result in what you described.
As for customer support it's always best to give a full explanation to the customer. Say for example, they honestly DONT have control over how the software associates IPs and VirtualHosts they could have explained that a software upgrade was performed and this is just the way things will be from now on. Its always good to counteract a negative with a positive, they might have suggested for example switching one of the sites to a seperate dedicated IP address or any other workaround if there is no possibility for a fix.
So there you have it
I wouldn't blame the host much but in every situation there's a good way and a bad way to handle it.