Yes, exercising ISOs causes AMT adjustments and possible AMT.  That's the whole point.  The stock then has a higher basis for AMT purposes, so when sold the AMT adjustment reverses and your client may get the additional tax paid back via the minimum tax credit (Form 8801). 

It goes on the W2 if it's a disqualifying disposition but the AMT already paid doesn't factor into the income reported on the W2.  You track the increased basis for AMT and there will be a negative AMT adjustment on the 6251 line 2k in the year of sale.

Each share has an increased basis amount for AMT purposes and can be accounted for separately.