No, it shouldn't be that difficult. There's a few possible causes for your problems:
1) You just added Facebook functionality to your site. Depending on the site and content, it can take a few days for Facebook too truly allow Like's to be clicked. That's because they want to scan a lot of the pages and check for malicious, spammy, or otherwise 'bad' content. Until then, the Like button will 'unclick' itself immediately, which is what I think you were mentioning was happening on some pages. A partial solution to this is to run some of your pages through their Debug Tools:
developers.facebook.com/tools/debug
That will manually fetch and have Facebook scan the page and should make the Like button work on that page (if there are no errors reported). It will also help them in their effort to get a warm, fuzzy feeling about your site in general.
2) The confirm popup usually occurs on sites/pages where there has been spammy/malicious content detected in the past. Facebook shows the confirm button to make sure that the user wasn't tricked into clicking the button (or didn't really click it at all). If your site never had Like buttons on it, that's probably not the case for you.
Hope that explains, and hopefully, the debug tool will help you get a few pages going while the rest are slowly (and automatically) checked out by Facebook. Let us know if you have any other issues though.
Thanks,
Alex