There are more competent people than me to answer this, but I had a similar problem, so I'll try to help. There are a few frames at the beginning of the Ditto fight where you can catch it and all your inputs matter.

1. make sure Bulbasaur's NOT in red bar, it makes it possible to act during the cry and messes with the frames
2. don't mash buttons during the "Ditto has appeared!" message, try to time your A pressing to be as frame-perfect as possible
3. make sure you don't let go of the up+a buttons too early while throwing the ball, I'd recommend holding it at least until you see it get in the ball
4. remember to nickname your Bulbasaur a one letter name It's a difficult trick, I've done over 100 runs now and I dread it still, I'm chuffed when I get it on the first try. I'd advise you to get to that point of the run and practice just getting Ditto in the ball. It's frustrating because you won't know you're doing it right until you do it right at least once. If you need a run with inputs to check if you're pressing the correct buttons at the right times check out Shirokami_Cusp's.

Btw. What are you playing it on? If it's an emulator is it set up properly? Check if it's not skipping any frames, that could be making your life unnecessarily complicated.

There are many people more qualified to answer your question than me, but since I have also recently started to run this category and had the same problem I think you may benefit from another rookie's perspective on the matter. Everything you do from 'power on', matters, first to consistently get the Ditto encounter and then to capture it. My guess is that you're just not doing things as quickly and precisely as they should be done. I'd suggest to watch some run with inputs showing(Shirokami_Cusp's works) and compare them to what you're doing. What helped me was:

• make sure you don't move before saving in Cerulean Cave
• make sure you're hard resetting and not soft resetting
• for the frame perfect walk-up to Ditto you can generally change the direction key when the character has begun walking onto the last tile before turning(you can't hit any walls or stand still, that will mess up the manip)
• follow the exact path as in the runs(and the tutorial)
• after getting the Ditto encounter try to dismiss the "Ditto has appeared" box as frame-perfectly as possible, it takes a bit of practice
• what I found helpful was to hold down+a during the cry, up+a immediately after the menu click and keep holding up+a until it gets in the ball(holding it that long is not necessary, but it prevents you from releasing it too early) I'd advise you to just play the run not paying attention to the timer up until that point, save after entering the cave and just practice this segment until you get it. The frustrating bit is that you'll only know you're doing it right AFTER you've done it right at least once, so up until that point you'll constantly be wondering if there's something you're still doing wrong. It just takes practice I guess, but if my 'advice'(re-iterating the tutorial, let's be honest) doesn't help you then maybe somebody with a bit more experience will be able to assist you. Keep trying, you'll get it eventually!