Missing Episode: The episodes "Tiger's Battle with Destiny" and "The Battle with the Big Bad Four". Despite being important to the plot, they were never shown in syndication.
Network to the Rescue: The syndicated BKN broadcasted the anime early weekday mornings, and only reran (repeatedly) the first season. Fox Kids not only ran the first season on it's Saturday morning line-up, but also broadcasted the second season. Unfortunately, they only ran the second season in full once.
ABC Family (at the time, Fox Family) however did run the second season a few times. However, for some reason, they never aired "Tiger's Battle with Destiny" and "The Battle with the Big Bad Four".
No Export for You: The first DS game was never released outside Japan. However, its sequel was released in August 2010.
The same can't be said for Monster Farm Online, the MMORPG. Even if you go through the trouble of singing up for a Japanese account, you can't play it because it blocks all foreign IPs.
Golem's voice actor changed midway through season 2.
Post Script Season: The third season was produced after it was Un-Canceled. And after the shock of the second season's ending, the third season was... a jarring shift, to say the least.
Screwed by the Network: The first season was rerun into the ground, and the second season was only aired in full once, with two episodes swiftly being removed from rotation afterward: "Tiger's Battle with Destiny" and "Battle with the Big Bad Four": the final confrontations with Gray Wolf and Naga. The third season was dubbed but never aired in the US.
Sequel First: The original Monster Rancher never came out in PAL regions—instead, its sequel, Monster Rancher 2, came out first with the number dropped. This caused certain aspects of the anime and the spinoff games to become cases of Marth Debuted in Smash Bros.—the Dino species were MR1 only.
Similarly, the original DS game never came out in English. English-speaking markets got DS 2 instead, with the similarly-dropped number.