General alternatives:
* Have an issue with: "I have an issue with the way this is being handled."
* Have concerns about: "I have concerns about the safety of this plan."
* Be troubled by: "I'm troubled by the lack of communication."
* Take exception to: "I take exception to your tone."
* Find fault with: "She's always finding fault with everything I do."
* Object to: "I object to this proposed solution."
Alternatives focusing on seeing the problem:
* Recognize a flaw in: "I recognize a flaw in the design of the system."
* Identify a weakness in: "I identified a weakness in their argument."
* Notice a deficiency in: "I noticed a deficiency in their skills."
Alternatives focusing on being the problem:
* Present a challenge to: "This new policy presents a challenge to our current workflow."
* Pose a difficulty for: "The lack of resources poses a difficulty for our team."
* Create an obstacle for: "The weather created an obstacle for the hikers."
* Hinder: "The traffic is hindering our progress."
More informal alternatives:
* Have a beef with: (Informal) "I have a beef with the way they're treating the staff."
* Have a bone to pick with: (Informal) "I have a bone to pick with you about that comment."
Remember to choose the phrase that best fits the context and your intended meaning.