It highlights the problems faced by social networks trying to set boundaries for what users can post.
The National Cannabis Industry Association said it was seeking "clearer guidelines" from Facebook.
Affected businesses should appeal to have their accounts restored, the NCIA told the Associated Press news agency.
The problem had affected all of the nine US states that had legalised recreational and medical cannabis, deputy director Taylor West added.
"The issue seems to pop up and then go away. These rules are applied extremely inconsistently," she told the BBC.
Facebook does not allow content that promotes the sale of marijuana regardless of state or country.
"In order to maintain a safe environment on Facebook, we have community standards that describe what is and is not allowed on the service," it said in a statement.
TV and radio advertising about legal marijuana is often restricted, meaning social media can be a vital way to communicate with customers.
Leah Levington, who owns cannabis business Enlighten Alaska, told AP the take-down was "frustrating" and she was worried her Instagram account could also be shut down.