Sleepy, i completely understand what you are trying to say. Sometimes, some of the characters in text do have a line missing or whatever, like as you said you have seen 'Sa' written like a 'ki' with a lower line missing.

This just entirely depends on the text you are reading, in Japan or any Japanese literature they may have or you get may use the full character or have as what you have noticed 'a missing line' or whatever throughout the character.

Nothing much can be done about it since it comes down to whichever book seems to do this, id try learn the characters as a full so if you do come across text where the character has a line or so missing that you will be able to recognise it.