I think that the fossils are as such by reason of intelligence.
Biblically it is plainly obvious that some creatures were more intelligent than others.. eg. the serpent was more cunning...
In order for myself to take my theory further on this subject
I wonder what the behaviours of animals would be during a rainfall to a flood of such magnitude.. I would imagine that earthquakes would have been happening as well.
Again I say it is a matter of intelligence.. would not the more intelligent creatures go for higher ground?
The large discrepency would be do to this factor, birds would have flown to higher ground, correct me if I am wrong.
Is it a natural instinct to survive in all of the animals? seeing that the major activity of covering creatures would be happening under the waters of the flood easily explains the discrepencies in numbers.
Look at Ezikiel 26:19 and on to the end of the chapter.. ;compare this to Numbers 16, in this Numbers story Korah and his brothers where swallowed up alive into the ground... Now look at the Genesis account for the flood, in chapter 7, the great deep burst forth, and the floodgates of the heavens were opened...
I imagine it looking something like this;
It starts to rain, Noah and his family went into the Ark, the people like normal people except maybe a few retreat to there homes seeing that it is raining quite hard(the bible does not describe wether it is violent or not but I think it would be safe to say it was very)...
At what point would they have realised they were in a great trajesty like none before it? A week? 2 weeks?
I could imagine the panic of the animals being prior to the humans. all the places on the lower parts of the earth would have started to flood and maybe right from square one... non the less any intelligent being goes to higher ground but the account says that the waters covered even over the tops of the highest mountains.(what were the hieghts of the mountains than compared to now?)
how long can a human hold onto a floating device in raging storms? and for how long can he survive without food?
any of the animals including humans that went to higher ground would most likely have not been fossilised because of the lack of mineralisation and quick covering, they would most likely have decomposed fully to the earth..
For the matters of the humans I have to say look again to the Ezekiel account and the Numbers account that I alluded to earlier.
Praise God for he will make the weak strong and confound the wise with the simple.