Sounds like you’re describing confusing the transitive and intransitive verb pairs. Remembering which was which was really difficult for me, but what helped was two things. A lot of the verbs follow a pattern as to which is the transitive and which is the intransitive, like in this table:
http://nihongo.monash.edu/ti_list.html
So I made a table of my own, slowly adding each verb pair as I learned them. The other thing I did was try to use each word in a sentence. When I did that it was a lot easier to remember, because I could think back to the meaning of the whole sentence instead of trying to remember if the word was the transitive one or not. There’s also a plugin/script you can use that adds example sentences from anime to each lesson item. That might help too.