Yes. it shall be disallowed! "Employee" contribution is governed by sec 36(1)(va) and not by section 43B.
The relevant extracts are as uder:
..."[va] any sum received by the assessee from any of his employees to which the provisions of sub-clause [x] of clause [24] of section 2 apply, if such sum is credited by the assessee to the employee's account in the relevant fund or funds on or before the due date.
Explanation.—For the purposes of this clause, "due date" means the date by which the assessee is required as an employer to credit an employee's contribution to the employee's account in the relevant fund under any Act, rule, order or notification issued thereunder or under any standing order, award, contract of service or otherwise;"
Only if incurred before due date of filing the return under sec139(1). Employees deduction not deposited on or before the due date shall be disallowed even if entire expense is incurred before the due date of filling of