I started my job mid August & mid September I went to a doctor appointment and found out I was pregnant and the the following week I found out I was actually 3 months pregnant. Would my pregnancy be considered pre-existing even though my pregnancy wasn't diagnosed until after I had already been working for my employer?

It depends on the terms of your short term disability policy, which we don't have access to here. If you don't have/have misplaced the plan documents, you can get copies from your HR department.