I think this is a good point. They didn't stole you 3 million USD, but much less. In 2016 bitcoin was not even 2k USD... anyway, that is still a lot of money.
The price in 2016 was between $400 and just under $1000 at the end of the year, and if the OP then had some significant traffic on the ATM, he might have overlooked that someone stole a few BTCs from him. Anything more than that only makes sense if the OP was completely unaware of how the whole thing works and the manufacturers of that ATM took advantage of it.
However, if in 4 years you do not notice that you are missing as many as 59 BTC, then I wonder if the OP is doing this business legally and does it have bookkeeping at all.