I've seen kennels advertised for €15 per day so €46 isn't totally off the wall. Although your dog only spent 2 nights in the kennel, the space was occupied for 3 days (i.e. another dog couldn't use it), so maybe that's why the cost was so high? I recall using a cattery that did this - charges were per 24 hour period not per night (bit like the airport carpark!).
What were you paying for your 2 dogs up to now? Maybe there was a special offer for both dogs together and you didn't realise it until you left in one dog only?