Why did Jesus ask his disciples to collect the fragments of bread in baskets? Why did Jesus asked his disciples to collect the fragments of bread in baskets?

As per scripture Jesus ask is disciples to collect only the bread fragments only,
but not the bones or flesh of the fish....
While the synoptic gospels (Matthew, Mark and Luke) are not clear as to whether the fragments were of bread alone (they only mention 12 baskets of leftovers), the gospel of John indicates that the fragments were indeed of bread. 

Quoting John 6:13 from NASB translation:


  So they gathered them up, and filled twelve baskets with fragments from the five barley loaves which were left over by those who had eaten.


It is the same with KJV and NIV translations. See parallel view of all three translations.

And the reason why Jesus asked the disciples to gather the leftovers is found in the previous verse, John 6:12


  When they were filled, He said to His disciples, “Gather up the leftover fragments so that nothing will be lost.”


Jesus wanted all the leftover fragments to be gathered, but the leftover fragments in this case only happened to be fragments of bread. (The crowd must have really loved the fish!)

And note that the bread and the fish were given by a lad (John 6:9) and Jesus gave thanks to the Father for them (John 6:11), blessed them (Matthew 14:19), broke them (Luke 9:16) and asked the disciples to distribute them.

The message Jesus wanted to convey was that: What is given to Him will be received with thanks, blessed, broken and be used to bless others. Nothing of what is given to Him will be wasted.

Another thing we learn from this is indicative of the principle we find in the life of Jesus: He was not wasteful. And He wanted His disciples also to learn this principle from Him.