Ever since my wife started with her company 3 years ago, her taxes have been messed up every year and not accurate according to what we stated on the w4 to be withheld, ESPECIALLY for 2013. I did not make much more than her and we filled our w4's out the same, yet my fed income withheld is more than double hers somehow. this of course means we did not have the correct amount deducted from her checks resulting in us owing money come tax time. 2 years ago he lost her w4 and im pretty sure he did the same this year. he claims to take the same amount from every check she gets even though every check is a different amount and there are no paystubs to verify this since he pays his employees in personal checks.
to make a long story short I need to know if there is any way to rectify this or are we going to be stuck paying for a 3 year in a row when we def cannot afford this.

p.s. basically his entire business is under the table and shady and I have already reported him to the IRS due to getting her w2 well after the legal deadline and only when she asked for it.

thank you for your help in advance.