It is a contract question first and an immigration question second. Nothing in the TN rules obliges the employer to bear costs, but a pay arrangement that shifts fees onto the employee can affect whether the offered wage is real and whether the agency is behaving like an employer.
Separate the government charges from the agency's business model
The direct government cost for a Canadian applying at the port of entry is the admission processing charge, and for an employer filing Form I-129 the amounts are set out in the USCIS fee schedule, Form G-1055, which should be read rather than quoted from memory. Everything beyond that is the agency's own overhead: credential evaluations it may request, legal drafting of letters, and its placement margin. An agency that recovers those from the applicant's wages should say so in the written contract, and the applicant should compare the net salary with what the letter states, because a letter that promises one figure while the deductions produce another invites questions about the employment offer's genuineness.
Ask for an itemized list of what is deducted, for which purpose, and whether the deduction stops when the placement ends. A cheap placement that leaves the applicant invoicing as a contractor is not a saving; it is a refusal waiting at the border.