This is understandable. The human brain is a pattern recognition machine, and your internal pattern recognition for WaniKani’s vocabulary is to recognize it during reviews. In order to recognize it in different contexts, you need to be exposed to it in those other contexts. And it needs to be done repeatedly, so the patterns become internalized.
This is fairly normal. But memorizing grammar from grammar resources won’t prepare you for seeing the grammar in native material. You need to read (or listen, or watch) native material to build up recognition of the grammar used in various situations.
This is common. For some people (such as myself), learning about grammar in this way gives you a general concept of the grammar, but that doesn’t mean you’ll remember it, or recognize it when you see it. However, N5 grammar and vocabulary are very common, so once you start reading (listening, watching), you will encounter them often.
Over time, you will internalize them. The process may be fast, or it may be slow. But eventually you will start to recognize and understand the grammar without even thinking about what it means in English/your native language.
Different people learn differently. Some people learn better reading up on a lot of grammar. Others don’t. Some people can dive right into native material, looking up grammar and vocabulary as they go, and learn that way. Others need to begin with graded readers and slowly work their way up.
That said, I will always recommend the Absolute Beginner Book Club as a starting point to try.
And I routinely give the following disclaimer: The first time you try reading a native material, such as those in the ABBC, it will be very difficult. It will be a struggle to follow along. It will be difficult to keep up. But if you stick with it, and if you ask questions, and if you read all the discussion in the club threads, you will come out on the other side recognizing that you made progress.
Just reading one volume of manga isn’t going to have much impact on your ability to read another manga. But it’s enough to prove to yourself that you can do it, and the grammar you will have learned along the way will give you a much stronger foothold for the next thing you read.
Maybe jumping into an easy manga or simple children’s book isn’t going to be what works for you. But keep it in mind.
Personally, when I originally tried reading manga, I found it too hard, and gave up. Multiple times. I would be so much further along in learning Japanese had I not given up those times.