Not at all common but not unknown. Indeed this very same question was asked on Fixya
By tom33834 on Dec 03, 2009
http://www.fixya.com/motorcycles/t3564846-yamaha_r1_07_battery_polarity_backwards
I do know of someone else that has also had exactly the same issue. In that particular case the original battery had be charged with reverse polarity when it had been charged for the very first time.
I would suggest you get a multimeter / DVM (Digital Volt Meter) and check the actual polarity of the battery - even though it is "flat" it should still have some residual voltage even if it is not the full 12 volts -
with Red meter lead to Red battery lead (and black to black) check the display to see if the reading is "correct" eg 11.45 and NOT -11.45 (note the MINUS sign)
If it IS correct (which is correct FOR THE BIKE) then that would be WRONG for the BATTERY markings and would definitely indicate a reverse polarity charged battery.
When you go to charge it keep it the same way round - charge as per the bike's polarity.
HOWEVER if you ever buy a NEW BATTERY do not fit it as per the old one - you will almost certainly blow some fuses and maybe more.
On a further point, if I remember correctly, to fit the battery "the wrong way round" the -ve terminal is on the righthand side of the bike and to get the red +ve cable to reach the battery will be sitting in the upright position - that is the TOP of the battery is at the top.
This is NOT how the battery should be fitted because if you turn it around as it should be (ie RED to +ve) then the battery lead is just not long enough and won't reach. When correctly fitted "the right way round" the battery is actually laying on its side with the top of the battery pointing towards the back of the bike.
If you know anyone else with an R1 perhaps you could have a look at theirs and compare it with yours.
Hope this helps
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