He did make an apology, but he did it with difficulty.

It means you made an apology because you were forced to, but to answer fully and correctly we need the full sentence or paragraph​.

It means: "I was forced to make an apology. I thought it was unfair. I didn't want to make it. Part of me was trying to speak. But the part of me that did not want to apologize was trying to stop me from speaking. Forcing myself to speak when I didn't want to speak, felt like forcing myself to speak with something blocking my through. It felt almost like choking."