Blockchain.info does have quite a few problems.
Besides showing negative amounts and a few other minor bugs, not showing transactions also happens quite frequently.
The fastes way to sort things out would be to check the status of the transacton on different block explorers. Blockchain.info is not reliable.
You might consider using a wallet where (only) you have access to your BTC's (non-online storage).
There are quite a few available for each operating system. The most commonly used (lightweight) client is
electrum.