General:
* Clashing with
* Disagreeable with
* Having conflict with
* Having difficulty with
* Being at odds with
* Being incompatible with
More specific:
* Feuding with: implies a more serious or long-standing disagreement
* Bickering with: implies frequent arguments over small matters
* Having a strained relationship with: implies a tense and uncomfortable connection
* Being estranged from: implies a complete break in communication or connection
Formal:
* Having a breakdown in communication with
* Experiencing interpersonal difficulties with
Informal:
* Not seeing eye-to-eye with
* Rubbing each other the wrong way
* Not hitting it off with
* Not being on the same page
The best word to use will depend on the specific situation you are describing.