Yes, the site is right.
But in a slightly different wording, but it could be slightly different sense as well:
I thought that it was just me that had the same thinking.
That is, what you said "eu pensei que só eu tivesse pensado nisso" and "eu pensei que só eu tivesse tido o mesmo pensamento".
As you see, they could mean the same thing, and then it could be a similar thing, but not necessarily the same. Even in Portuguese.