Losing Apps during Updates on IOS7

Ok, so I got an Iphone 5s as a replacment for my Iphone 4. I backed the iphone 4 data up and restored the data on the 5s. However after it restored all the apps some apps (3-5) were missing. Thinking it was just an itunes problem i ignored it. However the other day the iphone downloaded the new update and i installed it (this was done all through the phone) and when it restarted i went to look for an app (which was ifruit) and it wasent there. I was defently there before i did the new update (via phone) but after it was gone. I dont want to lose any more apps due to updates, is this a bug im just getting or is it another IOS7 bug and how can i fix it. The ones i lost during the tranferring were fine as they were simple 4-10 MB size but ifruit was 400 mb and i have bigger apps with important save data.