Canon 650d - Issues with MF through the Viewfinder

Good afternoon,

I am new to the DSLR world and have just bought a Canon 650d with a 40mm STM Lense, primarily for its new features for shooting Video. My background is in film. I would appreciate some help from the more experienced DSLR users of these forums. I have been out and about shooting in my local area and have noticed some inconsistencies when focusing.  For example,  when I am trying to focus on a subject, I seem unable to manually focus on anything when I am looking through the viewfinder.  What confuses me though, is that when I switch to Live View mode, I can focus perfectly fine. It is also worth noting that AF works perfectly through the viewfinder. So I might focus on a subject using AF, switch to MF and I am unable to replicate the focal point manually. So basically, my MF doesn't seem to work when I look through the viewfinder.  Am I being stupid?  Or does this seem highly irregular to everyone.  This is consistant when shooting an array of subjects in an array fo environments, so it is difficult to be specific regarding settings etc

I am here as a novice seeking help, so id appreciate it if people respond as such, and not make me feel stupid.

I thankyou all for your time and effort.