Ok, stop worrying friend, there is no issue. I'm telling you first hand because I noticed something similar, spoke with a GM like 20 min and finally understood what he was trying to tell me. I'll summarize it below to help you see the light.
I start pvping around midnight. At that time, I had 68k HPs. I hadn't pvped that day so 0 on the daily counter (let's call it DC) and let's say 3k on the "yesterday" counter (let's call it YC).
I pvp a bit and around 1 am I have 68k total, 1.5k on my DC and 3k on my YC.
Around 1:30 am, I have 68'0150 total, 50 on my DC and 150 on my YC.
I think to myself "WTF, I LOST about 2k between 1 am and 1:30 am".
What the GM explained to me is the following:
Around midnight, Blizzard starts the program to calculate the points gained during the previous day and this takes long. All HP gained during that time might not be taken properly into account and that's what happened to my 2k earned between midnight and 1:30 am. This is why those 2k points showed neither on the YC (only 150) nor on the TC (only 50). And they were not even in my total which was still at 68k.
BUT those points are not lost. They're just accounted for the next day. And this is confirmed, since the next day I made only around 2k... but my total went to 72k (i.e. the "lost" 2k from the previous day reappeard there).
So, yeah, the system is somehow flawed but take heart knowing you don't "loose" points, sometimes it just takes one more day for them to be properly accounted for.
nostra