I take it you are using a page builder such as Divi, editing pages with the page builder, and inserting dynamic content into the page content via shortcodes.
Except, because of certain compatibility issues Toolset introduced a custom form of shortcode, using the {!{...}!} format instead of normal square brackets, and Relevanssi doesn't recognise the custom format as shortcodes and they are not expanded.
I think the only way to resolve the problem would be to edit the content where you have inserted these custom shortcodes and replace the custom format with normal square brackets. I expect that they will then be expanded when displaying the excerpts.
You'll want to verify that they stilll work as expected in the original context.
