Steps to reproduce the issue

Create two (or more) taxonomies have node with same title.
For example:
I created two taxonomies that are: Language and Variant.
Both taxonomies have one node with title "notset"

Then I created a filter and select all nodes from these both taxonomies.

Expected result

The search results displays all items by default (since all nodes selected)

Actual result

Display only some items, because the Search modal merge node by their title, so the query not include all ids of selected nodes.

System information (as much as possible)

Additional comments

To resolve this issue, I modified the file below:
components/com_finder/src/Model/SearchModel.php

Replace the code line (line 194):
$taxonomies = \call_user_func_array('array_merge', array_values($this->searchquery->filters));

With below one:

//$taxonomies = \call_user_func_array('array_merge', array_values($this->searchquery->filters));

$taxonomies = [];
for ($i = 0, $c = \count($groups); $i < $c; $i++) {
    $taxonomies = array_merge($taxonomies, array_values($groups[$i]));
}

Please check this issue, and I hope that you can apply this fix to the next release of component.