Sub quesry manual filter are not working properly on basic model

Check above screen shot.
I have added multiple sub query base filter (Based on Junction Object) .
Same filters I have also added on aggregation model and basic model.
This filter working fine individually but when I am applying two filter at same time on basic model it is not working but same filter are working on aggregation model.
I had check all the conditions both the model have same conditions.

Please provide workaround or solution for this.

Can you post screenshots of the condition configuration and the filter configuration.  

Also can you confirm several things. 
- The two models are based on the same sObject. 
- The filters and conditions for the two models are EXACTLY the same.