Hi, thanks for the report, but I can't reproduce this issue: https://i.imgur.com/hOv79fh.png. I got the above on a completely new world with Bob's ores (forced to generate all possible ores), so it seems to be fine.
NB: From your description, it sounds like you're expecting the new shortcut to work the same as the old tool, i.e., just click. Instead, the new tool is a blueprint-like selection tool: you must drag-select at least one ore entity for it to work.
This is not specific to Bob's mods and must be done for any resources. On the bright side, drag-selecting makes it easier to add oil sites.