I am also having the exact same problem with my site (https://gbapps.net) my site has two downloading servers and I am having this issue how can fix this issue because I have search a lot and I have found nothing helpful.
Hi @harrycallum, and welcome to the LE community forum 
The simplest (although not always available) method would be to have each server get its' own cert via DNS authentication.
The tricky part with DNS auth is that it requires adding TXT record(s) into the DNS zone [preferably in an automated fashion].
Automation requires the DNS service provider to support updates via API [this part is not yet an industry wide supported feature].
And you would have to use an ACME client that supports DNS API updating [this part is easy].
If DNS auth is not available to you, then you would have to get creative on centralizing the process of obtaining the certificate via HTTP auth and then securely sharing the certs to all your servers in an automated fashion. [not impossible, but there isn't much along the canned software choices for that route - read: requires "custom programming"].
I'm sure you will have questions...
Feel free to reply with as many as you can carry!
And we'll try to lighten that load
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