The alleged incident occurred during Gold Coast's VFL match against Brisbane on Saturday, with the matter referred to the AFL's integrity unit.
If found guilty, Knobel - who is yet to make his AFL debut after previously spending time on Fremantle's list - would face a sizeable ban.
The AFL have been forced to act numerous times over recent years in their bid to stamp out homophobia.
Earlier this year, Brisbane Lions draftee Koby Evans received a four-game ban for directing a homophobic slur towards a VFL opponent.
That came less than a fortnight after the league sacked its appeals board chairman Will Houghton after he said racist, sexist or homophobic language was "commonplace" in the AFL.
Houghton made the comments while adjudicating a case involving St Kilda's Lance Collard.
Collard, who received a six-game ban two years ago for using homophobic language, was initially handed a seven-week suspension for another incident this year before it was reduced to two weeks on appeal.
The 21-year-old claimed he didn't use a homophobic term in this year's alleged incident.
Adelaide's Izak Rankine was banned for four matches last year for using homophobic language, missing the Crows' finals series.
Untried Sydney defender Riak Andrew (five matches) and West Coast player Jack Graham (four) were also suspended last season.
In 2024, ex-Port Adelaide player Jeremy Finlayson was handed a three-match ban, and Gold Coast midfielder Wil Powell was suspended for five matches.
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