Unless your employer is the government (or local government), I don't see how anything your employer gives you could be considered "public funds". But the fact that the vouchers are paid free of tax, I can see why this could be confusing. Having said that, if this is a tax credit to which everyone is entitled then it doesn't count as "receiving public funds". Check the link provided by @Traveller about public funds: https://www.gov.uk/government/publications/public-funds--2/public-funds
As suggested in a comment, you need to talk to your employer (their accounting department, or possibly HR), to clarify this.
If it is determined that the vouchers are not allowed, then I think you need to tell your employer to stop giving them to you, and return any you have already received. Get documentation to say that you did this, if this is the case (in case it comes up later).
As long as everything is above-board, it should not affect any future immigration-related processes you go through, such as ILR or citizenship. It sounds like the employer instigated this scheme, and not you. The fact that you questioned it can only go in your favour if it ever comes up.