Hi Noktavontavius, Welcome to the forums.
I’m sorry to hear this issue has occured for you in your save. We have a known issues report on it here: [Known Issue] "Who Needs the Sea Anyway?" Trophy Unlocking Issues which contains some workarounds including the one Dank-a-licous mentioned about traveling to a new island and planting there one after another.
If you continue to have issues please post a new bug report with as many details as possible in the Console Bug Reports section. We ask players to avoid reviving older posts as sometimes there’s newer information available and it also prevents your report getting missed in a comments section 
Thank you!