To say nothing of the intentional release of design variations. For instance, Patti the Platypus comes in several almost-indiscernible color variations; Mystic the Unicorn had three design changes; Lucky the Ladybug can have 7, 11 or 21 spots (and they can be stitched-on felt or patterned fabric!).
Name's the Same: A couple Beanies have identical names despite being different species:
One of the early Beanies was Bongo the Monkey, formerly Nana. Later on, there was an orangutan Beanie also named Bongo, and a bear named Nana.
Fearless is the name of both a guinea pig and bulldog Beanie, although the latter was a UK exclusive.
There are two different dog beanies named Fetch. One is a golden retriever, and the other is a generic gray and white dog. Adding to the confusion, there is also a brown dog Beanie named Fetcher.
There are two nearly-identical Ty-dyed bears: Groovy and Groovey.
Two different bunnies are both named Hippity and Hoppity.
...to say nothing of Nibble, Nibbler, Nibblies and Nibbly. Four different bunnies with almost the same name.
Both a gold bear and hamster are named Pecan.
There is a pink flamingo named Pinky... and a pink guinea pig (of all things!) named Pinky.
Two different dogs are both named Rowdy.
A pink bear and pink hedgehog are both named Smitten.
No Export for You: Several Beanie Babies, Beanie Buddies, and Classic Ty plush are ONLY available in certain stores, in certain countries, or at certain events.
There's a Loch Ness Monster beanie named "Mystery" who is only available in Scotland.
The earliest example of this is a bear named "Maple" that was only available in Canada.