I was let go from a job and had to wait 90 days for health insurance at my new job was covered for those 3 months by the old job?
You are only penalized for the full months in which you don't have health insurance. If you have less than 2 months without consecutive coverage then you won't be penalized for not having health insurance. Please see this link for more information: https://www.healthcare.gov/exemptions-tool/#/results/2016/details/short-gap