I wasn't able to reproduce this in a local 12.0 SP6 instance I have installed. Could you confirm which version of Aras Innovator you're using as well as which relationships grid you're testing this on?
I tested this in a local 12.0 SP1 instance as well and wasn't able to reproduce the issue. Could you let me know what relationships grid you're seeing this in? Is this a standard relationship like Part BOM ?