So, you've been having problems spelling inoculate. It just doesn't look right, having just one 'n', especially when you compare it with words such as innocuous.
Let's start with the easy one, innocuous. This is formed by in, meaning 'not', and nocuous meaning harmful (eg. noxious). Hence the double 'n'.
Inoculate is from in, this time meaning 'in', and oculus meaning eye (eg. ocular). The connection to vaccinations is that trees were inoculated by grafting foreign buds (eyes) into them, like grafting viruses into people.