Something like this has probably happened to everybody at some point. And there’s any number of reasons for it. Yeah, the FTP setting could be wrong: remember, the computer just takes 95% of your 20 minute power, which may or may not be your FTP. It’s a formula based on a model that approximates FTP for a good chunk of people, but doesn’t mean it approximates it for YOU.
Even if the FTP setting could is correct, you could still be having trouble. First, the Zone 4 workouts have an endurance component too, and you might just need to build up to 20 minutes at a time in the zone. Second, if you’re having trouble holding zone 5 or 6 power, remember that % FTP is a very bad way of prescribing workouts above threshold because everyone’s physiology is different and those energy systems don’t really relate that well to FTP. Third, as you say, you could just be tired, especially if you’re hitting the weights hard beforehand.
But in any event yeah, you can mess with the time or power setting as much as you need to to fix the problem.
If you’re fresh and you have trouble completing 2 x 20 but can get almost all the way there, the FTP setting is probably fine but you just might need to build your endurance. In those cases, i’d leave the power the same, but shorten the intervals as needed. Maybe do 2x17, 2x15, etc., as needed, until you get up to 2x20.
If you’re fresh and you’re having trouble holding Zone 4 for even 5 minutes, that suggests the FTP setting might be too high, and you’d be better off reducing the power until you can complete a longer interval. Just reduce it a little bit and try again, there’s no magic to it.
If you’re not fresh (for example post-weights) and have trouble holding the power, you might just reevaluate whether it’s worth doing a zone 4 interval workout that day vs. just pulling hte plug and doing something easier.