Tips with tracking?

Hi
I started using MFP last week, and bar a few days where I went away for a holiday (that involved eating several different types of caramel slice from a selection of cafe's and bakeries, as well as lots of swimming and walking) I've been diligently tracking, mainly using the auto search to find what I am eating.

Today I've been relying on the bar code scan function and scanning foods individually. I have a large deficit of 1000kj, particularly after my second work out where I recorded the kj burned from the counter on my bike (seems pretty accurate based on time/effort fluctuations in readings) instead of the auto complete on the exercise log.

Have I done something wrong tracking this way or have others noticed deficit when they start tracking more accurately?