It seems several things are going on here at once.

• You seem new to using PDAF through the viewfinder of a DSLR. There is a learning curve involved. It is just as significant a learning curve as the one encountered when moving from a compact, small sensor camera that yields almost limitless depth of field to a larger sensor camera that means the depth of field in most shots will be much narrower. You need to research and learn the unique characteristics of the PDAF system in your particular model. It will take some time and experimentation to master it.

• You are discovering the imperfections of Phase Detection Auto Focus (PDAF). When they first came out, PDAF systems were designed to be as fast as possible at the expenses of absolute accuracy. As technology has advanced over the past 25 years or so, the emphasis has shifted some to both fast and accurate, but this is mainly seen only in higher end camera/lens combinations. Entry level bodies and kit lenses still exhibit inconsistencies when PDAF is used. But the expectation of pixel-peeping-perfect-focus-every-shot in the digital age make them seem much worse than they did a few years ago when most photos were produced as small or medium sized prints and exact focus was nowhere near as critical!

• It appears reasonable to suspect that your EOS SL1 body needs the overall PDAF system to be calibrated. Again, higher end bodies allow the end user to do this via Auto Focus Micro Adjustment (AFMA) but the entry level Rebel/Kiss/xx0D/xx00D series do not. The camera will need to be sent to a Canon authorized service center to have the AFMA calibrated. Also send your most used Canon lens along as well.

• It seems your Yongnuo 50mm f/1.8 lens is even further out of calibration than your camera body, and in the same direction. It needs to be calibrated to your camera after the camera has been set at the factory service center. With third party lenses this can be a headache unless you are willing to send the body along as well. If one needs to send the lens all the way back to China for this, I would probably not recommend sending the camera along. For a lens this cheap it would probably make more sense to just: a) try another copy or b) get a Canon EF 50mm f/1.8 STM for practically the same price.