Yes, the equations feature in Google Docs is half-baked. You have two ways to address this:
Firstly, leave feedback for the developers so that they know that people don't like how this feature works. You can do that by clicking on the ? icon on the top right of drive.google.com, then clicking "Send feedback". Alternatively, in the mobile app, tap the menu, then tap "Help and feedback", then "Send feedback". Leave a description of how the equations do not work properly for you.
Secondly, I recommend that you learn LaTeX, which is a markup language for typesetting documents. It is specifically designed for including equations in a document, and the output from LaTeX documents is very neat, in most cases perfect. LaTeX is the industry standard word processor for mathematicians, scientists, statisticians and other professionals across the world—it is very widely used. You should learn it by reading Daly & Kopka's Guide to LaTeX, the packages documentation, and tex.stackexchange.com.
You can run a LaTeX editor on your computer and sync the files with Google Drive using a sync client (such as Backup and Sync or InSync) in order to make sharing them easy, and for a back-up. On Windows, I recommend installing MiKTeX, otherwise just install TeXworks. Overleaf is an online editor, which doesn't require installing a program on your computer, but it is slow.
The reason why I'm recommending an alternative word processor is because Google Docs is designed for simplicity, but it is currently not up-to-scratch for creating professional documents. You have more control over the output when using LaTeX. You can still use Google Docs when you don't need to waste time with delving into complicated markup language, or if you are collaborating with others, but Google Docs will generally give you simple documents that don't have a high degree of perfection.