Within the very limited facts that you presented... the bank cannot NORMALLY take funds from a corporate account and apply them to a personal debt. No more than they could take your personal funds and apply them to MY personal debt. The corporation has the right to protect its funds from fiduciary irresponsiblity.
Have the corporation contact the bank about the 'missing' funds and ask that the funds be returned and/or an explanation for the 'loss'. Then, if the bank refuses to return the funds to the corporate account, or is unable to provide a valid reason for their action, the corporation will have to fight for the funds return. This can be done by hiring an attorney and/or contacting your state banking commission and filing a complaint.