Can a deposition be extended when the attorney asking questions wasted time on irrelevant questioning?

There are two situations applicable to what you say. Both lead to the same answer: no. The first situation is as you describe: thoughtless actions by a participant and pointless questions. The other is that there were legitimate reasons for what looked like irrelevant questions to you, the deposition had already been approved for extended time, and something came up. Either way, a judge doing something about it is quite unlikely. If there are are legitimate reSons for a longer dep, even if you think otherwise, it will go longer. My view: the 3 hour rule was designed to prevent abuse. It also leads to abuse. Regardless of the reason, you were poorly treated. There is no excuse, none at all, for failing to prepare a witness for a known longer examination, and failing to accommodate an out of town lay witness. Unfortunately, that is just my opinion.

Mr. Cohen has provided a thoughtful and complete response. I agree with his comments and join him in sympathizing with your situation. However, the unfortunate result is that likely there is little you can do if you are a party. If you are a nonparty deponent, you may be able to seek additional witness fees but that would be only a minimal contribution to your additional expenses. Any new deposition should be conducted at your convenience to the extent possible.