It's true that computer "hiccups" can and do happen, and because you can never catch the computer in the act, it's next to impossible for anyone to figure out what is going on.
Keep in mind, too, that the store is using some e-commerce software that they bought. It's not as if the store owner or staff actually wrote the computer programs.
And techology is COMPLICATED! That e-commerce software was written in (pick a year)... meanwhile the webserver that it's hosted on may have had upgrades and patches to its software... not to mention all the different computers and browsers that shoppers are running, and all are at different patch levels and it's always changing, because there are software updates and anti-virus updates and nothing EVER stays the same for more than ... maybe a second. ;-)
All that said... I agree with sweetana3, that the bigger issue is that the store would not be flexible in view of the fact that you'd experienced a problem. Could be that you were talking to a lower-level customer service person who simply did not have the authority to adjust prices.