Free SSL Can Lead to HUGE Headaches

So you needed to manually implement the challenge? There wasn't just a button to press in your control panel? Because most of the time, a hoster which implements Let's Encrypt does so by providing a plugin in their control panel to take care of everything. Unfortunately, there are a lot of hosters not implementing such an automated system. If your hoster is one of the latter, you should change hosting provider to one which does provide automated implementation.

See the Web Hosting who support Let’s Encrypt thread for more info.

That's not something Let's Encrypt can prevent nor does Let's Encrypts certificate itself cause such a thing. Only your hoster can is to blame.

See FAQ - Let's Encrypt

What is the lifetime for Let’s Encrypt certificates? For how long are they valid?
Our certificates are valid for 90 days. You can read about why here.

There is no way to adjust this, there are no exceptions. We recommend automatically renewing your certificates every 60 days.

I guess you chose for a sub-optimal hosting provider. Unfortunately, this could be just the only thing they don't implement implement and you couldn't have known this before.