Last year my balance on my 401(K) was less than $1000 when I changed my job and fidelity issued me a check and withheld tax. I received 1099-R. Why should I pay penalty?

I was in a company for a short term and I paid 401(K) out of my paycheck. When I left that company and joined another company, my balance was less than $1000. Fidelity sent me an email saying if your balance keeps less than $1000, it will be against their minimum balance role and will issue me the total balance after tax.
I received the check and deposited it on my checking account. Now, I received a form 1099-R and I have to pay penalty due to pulling the money out from my 401(K) before I reach out the retirement age.
Since Fidelity withdrew the money not me, why should I pay 10% penalty?