I lost my job and my insurance coverage lasts until end of June. In the meanwhile, I’ve purchased temporary health insurance and in mid-September I will apply for standard insurance. I just want to confirm that I will not be penalized with the ACA fee since I will be covered with temp insurance for no more than 3 months. Please let me know if this is the case.
Losing coverage that doesn't count as minimum essential coverage, like short term health insurance, won't qualify you for special enrollment. You can however go less than three months in a row without coverage a year, during this time you can get short term health insurance or stay uncovered... but this is an aside, it doesn't override the rules about special enrollment. Therefore, it is typically the best idea to simply enroll in the Health Insurance Marketplace via special enrollment when you lose minimum essential coverage.
Losing short term coverage doesn't count as losing minimum essential coverage and therefore you won't have coverage options until open enrollment opens in November (and that coverage won't start until January 1st.)
In your case you should drop the short term plan after enrolling in special enrollment in the Marketplace or extend short term coverage for the rest of the year and prepare to pay the fee for the remainder of the months in the year.
Here is an instance where short term makes sense: You lose coverage in October and want a plan that will cover you until January 1st when your Marketplace coverage starts. That may make more sense then getting a major medical plan with a $13,000 deductible for 3 months.