It sounds like you're new to MMOs.

Sure it sounds easy on paper: test these things out first thoroughly, make sure they're all balanced and play as intended. Release a test server, even.

It doesn't play out this way. Every MMO has issues like this, even ones with test servers. People don't play on test servers the same way they do in game because that's not where their real characters are. Nobody would spend 18 hours a day for a week spamming hunts in a network of linkshells on test servers because they won't see any benefit; their main character is on X server.

In the case of hunts, SE didn't anticipate the community working together as much as they did. Again, hard to predict. They assumed people would be selfish, gather only as many of their friends/FC members as are required to kill the mob then kill it. Instead, people took the path of enlightened self-interest and shared the rewards. In so doing, increasing the rewards to all players beyond what SE has anticipated. It wasn't exploiting or breaking any rules, so it didn't require an emergency maintenance. It didn't break the economy as the rewards are all rare/ex.

SE can't anticipate what that one clever dick in the millions of people playing comes up with to circumvent their systems. They can do their best to try anticipate it, but they're never gonna succeed 100% of the time.