There is a cheat which may help. First make sure testingcheats are on. If you have UI Extensions Mod this is automatic.
Next shift + left click (PC) on the plant or dirt pile. Choose “Set Gardening State” and you will be able to control the weeds as well as growth. You will need to do this to every plant. To gain harvest do this before 5am the next morning.
If the weeds don’t clear, shift + left click “Reset object.” That will clear the weeds.
Hope it helps. I haven’t had this issue since the update. Check your mods and make sure they’re up to date.