If 1 of the push rods (see below) are off, the other one that is connected will be doing all the work and may cause things to go cock-eyed. The push rod cap is the weak link in the system so it breaks first, saving the gears in the transmission from breaking and causing expensive damage.
The end caps on the push rods are for sale, but it might be better to buy the entire push rod as they seem to bend quite easily. And there's a chance your working rod could now be bent, so you might need to replace both of them.
I just did this to an 09 Boxster S I purchased. The right rod was off and the top was going up and down using the left rod. It would make a knock sound in this scenario. I bought a new rod to replace the broken right rod but having the new one, it looked like my left rod might be bent even though it was still on the ball cap. So I bought a 2nd rod and replaced the left rod. It was definitely bent, as you can see in the pic.
Once I had two straight rods on, the top went up and down without funky noises and the clamshell fits tight.