I should have purchased 5900000 Helium Isotopes, but in reality, I only had 3550000
Just a guess: Maybe only that much was available for the specific price you tried to purchase but no more? 
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My guess is you purchased some at other stations and maybe other systems? Check personal assets and do a search. If you used a corporate wallet, then they are in deliveries.
When I do a bulk buy, I check the available amount at the current station. If it is not enough, I will advance down the list of offers.
For example…
If I am buying Kernite and I need 10,000 units, but the market shows me the following offers at the station.
5000 units @ 850
4200 units @ 880
10000 units @ 890
I will say buy 10,000 immediately @ 890 and it will grab the first 9200 and take the remaining 800 from the 3rd line. I pay a bit more, then I don’t end up having to place multiple orders.