PA taxes employees who telecommute but not for the convenience of the employer.  The employer either thought that IL has the same rule or your client did not file the appropriate withholding/exemption certificate with the employer.

Your client should have noticed this long ago.  Check with the employer whether it's still possible to issue a W-2C to move the withholding to PA.  If not, your client will need to file an IL-NR return for a refund claim and be out of pocket for a while with the PA balance due.