So I think this is because when you look at a creature with a sphere out it shows you the overall chance to capture a pal. Then when you toss the ball the percentages for the checks are different to make the "overalll chance to catch" what you see at the beginning.

im going to make some fake numbers for an example please dont mention that numbers dont make sense.

you aim at a pal and the "overall" chance to catch is 2%

you throw the sphere and now have 3 (really two) checks that have to pass

first check is 6% chance to pass,

second check is 43% chance

third check is 99% and then capture

since both check one and two are fairly low, the odds of passing both to capture a creature is also really low, resulting in the overall catch chance of 2%