I see what you mean now. I can't actually see the second example as it's blocked for some reason in the UK.
I had a problem when I first came across り written as a single stroke rather than the two strokes I originally learned.
They are just variations because they are different fonts or handwriting styles. Mostly it's a case of a character being written with a single brush stroke rather (joined up so to speak) rather than the brush being lifted between strokes. There's also a style called grass style that even Japanese can have trouble reading.
It's hard when you're learning to encounter a different style but I think there's less variation than with English letters. Have a look at an English type book to see what I mean.
You are sensitive to the variations because all the shapes are new and strange so any variation tends to look like a new character. Japanese on the other hand will know what "should" be written in a given word or sentence so it's less of an issue for them.
This post on reddit has some interesting points
http://www.reddit.com/r/LearnJapanese/c ... es/c1l1x3y
If your immediate problem is writing, find a clear model example to be written with a pencil. (A brush is hard to use properly)
If your problem is reading, with practice and exposure it gets easier.