Sorry for the delayed response...
No, we didn't do anything. It was likely a issue with LinkedIn itself, which does happen from time to time. The other possibility is the URL you were using to test the LinkedIn Apply button. Try from both
www.site.com and site.com (no www) and any other sub-domains you may have and verify that both work. If not, let us know, and we can help you get them both working.
Thanks, and good luck,
Alex