I'm guessing it only affects these HK junction objects? Looks like whoever made them set the road level at 0 metres rather than the usual 0.1 metres, so they're clipping into the terrain. Just set their height to 0.1 metres and all will be well again.
Don't mind helping, but it would get annoying for you to be asking about every single operation in the editor, especially when it would be faster to look it up anyway.
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