Its not a bug. bungie did this on purpose. read patch notes.
If anythings working fine, bungie will fix that for you.
Edit: correction, hotfix patch notes
https://www.bungie.net/7_Destiny-Hot-Fix---09242015/en/News/News?aid=13601
English
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Woo read the patch notes they fixed it bro
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yeah i saw the patch notes ^.^" well atleast i think they are trying to get things fixed properly lol.
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My farming method involves more than 20 chests being looted across the Drednaught one at a time and not twice per spawn. This hot fix should not apply to this sort of farming method.
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Patch notes: Some treasure chests in the Dreadnaught are now in a location that only allow them to be looted once per spawn I am only looting individual chests once per spawn. But after picking up about 7 chests, any new, individual, located elsewhere chests that I haven't even touched previously are completely empty.
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I was farming several maps on the dreadnaught and it stops. trust me, they want you to re enter the atmosphere and come back... this is all because of the hadium flakes being used for the moldering shards..