1. I assume that the bank was the original lender. Therefore, it would have owned the loan in the first place and would probably have had the right to use money in your other accounts towards the loan, if it was in default. It could have used the collection company just as a debt collector, or it could have sold your loan to the collection company - you need to find this out so that you know to which party you now owe the money. Maybe you should keep your savings in a different bank from the one that's lent you money.
2. Banks are heavily regulated and the collusion you suspect would go against the principles of 'Treating Customers Fairly', which is a key part of the financial regulator's armoury at the moment, so I don't think this is happening. It sounds like it's just down to poor administration, which doesn't surprise me. Get your bank statements, and if both November and December payments show as having come from your account (and have not come back) then the problem is the bank's/debt collector's and they should be told to sort it out. Banks can trace outward payments easily. The giving of the reference number is not a problem as this will help the bank/debt collectors trace the missing payment.