Question: When creating an Alias to a single article, the content editors keep making this mistake where they select an Alias which has the same/similar title to the 'Single Article' Menu item.

When an alias is pointing to an Alias, this causes a broken link since as alias can't be pointing to another alias.

Is there any way to not display aliases when the 'Menu Item Type' being created/updated itself is an alias? 

Or at the very least, is there a way to alter the CSS so that if there is two Menu Items being displayed with the same 'Title', the alias or the menu item gets highlighted so that it is obvious which is alias and which is a single article?

Answer: 
You can never save 2 menu items with alias. You will always get this message:
**Save failed with the following error: Another menu item has the same alias in Root. Root is the top level parent.**

Yes this can happen that your menu item alias and article item alias is same.

Are you creating a New Menu with *Menu type* as **Menu Item Alias** ?

Please if you can explain briefly your issue or add screenshots for this ?
Yes, it looks like there is a small bug in Joomla. 
You should not be offered any 'Menu Item Aliases' in `Menu Item` drop-down box when `Menu item type` is 'Menu Item Alias'.
It is not exactly bug, but something which could cause inconvenience.