People can write and spell and capitalize/capitalise anyway and anyhow they please.
If you want to get to the nitty-gritty, you need to decide the purpose and audience of your writing.
If you are writing informally about Pokémon (note well, the e in the word has an acute accent on it, thus é), then you can capitalize it as you please. I don't know who told you not to capitalize the word when it refers to a group of pokemon/pokémon, but there is nothing wrong or illegal about either capitalizing or not capitalizing it in this case.
On the official U.S. website for Pokémon, the Legal Page says
Pokémon, Pokémon character names, Nintendo 3DS, Nintendo DS, Wii, Wii U, and Wiiware are trademarks of Nintendo.
The Chicago Manual of Style (CMOS) (online version) says
Brand names that are trademarks—often so indicated in dictionaries—should be capitalized if they must be used. A better choice is to substitute a generic term when available... [emphasis mine]
Note also that some companies encourage the use of both the proper and the generic term in reference to their products (“Kleenex facial tissue,” not just “Kleenex”) and discourage turning product names into verbs, but these restrictions, while they may be followed in corporate documentation, are not legally binding. (In fact, Webster’s includes entries for lowercase verbs google and xerox.)
Examples of trademarks from CMOS include Bufferin (buffered aspirin), Coca-Cola (cola), Jacuzzi (whirlpool bath), Kleenex (facial tissue), Levi's (jeans) and Xerox (photocopier).
So, following CMOS, one wouldn't say
There's a bunch of kleenex over there
There's a bunch of Kleenex facial tissues over there.
By analogy, I guess one would say
There's a group of Pokémon pocker monsters over there.
The APA Style Guide (aka the Publication Manual of the American Psychological Association) says to capitalize trade names and brand names. I don't own an APASG, so I got that from the APA Style Blog article "Do I capitalize this word?" (link). The blog contains a chart of "noun types", amongst which is Product and that seems what Pokémon falls under, given that that type includes Advil, Xerox, and Prozac (brand names).
Neither source discusses the plural of a trade mark or brand name. Probably for a reason. There is no official, legal plural of a trademark unless that trademark is registered in a plural form.
Pokémon, as far as I can find, has only ever been registered as a trademark in the singular. When I go to the United States Patent and Trademark Office's Trademark Electronic Search System (TESS) and enter search string POKEMON, I get 97 to 100ish results, all in the singular. The search result times out after a while, so you will have to do your own search to verify my results. And if the above link to TESS doesn't work, you can access it through the page Trademark Database.
The International Trademark Association (INTA) supplies a pdf called "A Guide to Proper Trademark Use for Media, Internet and Publishing Professionals", which you can get at their Trademark Basics page. This handy publication provides "a few
easy-to-follow rules concerning proper mark use," namely
When referring to a mark, make sure you pass the “ACID” test of proper use
The A in ACID stands for ADJECTIVE. And the publication goes into a lot of blah-blah about why a trademark is a "proper adjective" and not a noun:
Trademarks and service marks are proper
adjectives. Not nouns. Not verbs. A mark should
always be used as an adjective qualifying a generic
noun that defines the product or service. A
mark is a company brand name, not a product or
service itself. As adjectives, marks should not be
used as plurals or in the possessive form, unless
the mark itself is plural or possessive (such as
1-800-FLOWERS, MCDONALD’S or LEVI’S).
This advice to the media is actually meant to help a company such as The Pokémon Company protect its legal registered trademark. Because if people start nouning it and verbing it, the company risks its trademark/brand name becoming so generic that it becomes difficult for the company to maintain its trademark. Trademarks that have suffered "genericide" include Aspirin, Zipper, Kerosine, Corn Flakes, Elevator, Escolator, Heroin, Thermos, and Yo-Yo.
Xerox put out an ad basically begging people not to use xerox as a verb: If a trademark is misused it could become undone. See Legal Blog Watch's Xerox Ad Pretends We Care About Its Trademark Rights to Term 'Xerox' and also BBC News Google calls in the 'language police'.
So, I suppose that is why the official sites of Pokémon always (as far as I can see) use it just like that: Pokémon, which is the legal trademark, as a "proper adjective" and not a "proper noun," although The Pokémon Company is not always so careful, straying from the registered trademark in such a use as
The Pokémon Company and its worldwide affiliates are always striving to increase Pokémon's popularity in markets around the world [my emphasis].
It's ironic the next two words are "Brand management."
If you wanna be nice to the company, and also go by the CMOS, always always use only Pokémon and never pokemon. If you don't give a rip, spell it and capitalise it anyway you pleez.