Why can't I download certain tracks I purchased in iTunes?
Generally the iCloud symbol in your library means the file has yet to be downloaded, therefore it's absence also generally means that the file has been downloaded and is locally present. Try downloading the ones with iCloud symbols then doing your transfer.

If I am misinterpreting this and you can't transfer the files at all, whilst your iPad is connected there is a "Transfer Purchases" button under File > Devices in iTunes's menu bar to transfer files directly.