SSL installed but it has affected other sites on the server

Recently I installed an ssl certificate for a customer and after a while noticed that Google has got all other sites on the server mixed up.

Site A had the SSL cert applied. Site B started getting Google listings with the URL from site A.

For example, Site A has the URL "/sign-up", site B doesn't. After the SSL certificate was applied Google started indexing "/sign-up" on Site B.

What I have done to try to fix the issue:

1 - Give sie A a unique IP

2 - Used Google's "Remove outdated content" tool, this is only temporarly

3 - Updated the Robots.txt so Google shouldn't crawl the domains

Is anyone familiar with this issue and what can I do to stop Google indexing Site A's URLs on Site B/C/D/...?

Thanks in advance