It is true that sometimes uracil could be present in DNA.
Uracil is almost exclusive to RNA but in some cases deamination of cytosine can cause uracil to be present in DNA.
I believe what Chargaff proposed was very crucial in understanding the structure of DNA. It was way back in 1950 (Chargaff ratio gave the clue to the structure of DNA) and we've advanced lot more now.
Just like Markovnikov's rule (organic chemistry) gets opposed when a little re-arrangement of carbocation occurs.
Scientists just try to make things simple. Having exceptions to rules is nothing new in chemistry :)
Moreover, the answer to your question that whether Chargaff was accurate? From everything that was available for research that moment, yes.
I think we for now should have gratitude for what he's done.
You find it easy today because of the ratio. Imagine he hadn't proposed it because of this exception?