I used to be on a scheme where the lease was subsidised - the firm paid 5/7ths of the lease cost and I paid 2/7ths (the weekend portion). Whilst not quite the same as you have posted the pitfall may be similar.
On occasions we got offered really good lease deals Evoque as an example) when the vehicles were first launched. Cost to me was around £200 everything found. HMRC however took the view that the BIK for a top fo the range Evoque was whatever it was at the time and my BIK was the difference between what the car was worth and what I paid - which was substantially below the typical market rate for a lease.