I suspect that is some other code in your install that also hook into the WP_Query to alter the query with custom SQL. As far as I know, we always alias the tables when we use custom SQL for our filters, but I can check it out for you. Can you tell me the type of the column you’re filtering on? And do you only have this issue when you filter on this specific column? Or on other columns as well?
Could you also send me the SQL error in full to email@example.com so I can analyze it for you? You could also try to contact me on the live chat on our website.