When Windows is hibernated, it is just like the system is still up and running. When you boot Ubuntu and copy a file, Windows is unaware of the modifications you make on its back and still assumes that its NTFS partition hasn't changed since it was hibernated. In fact, everything you changed since then is considered as corruption and could cause serious problems in the filesystem structure, even running chkdsk could be a risk since it will try to make the filesystem consistent with Windows own view and will probably find that it differs.
NTFS-3g which is the tool that allows you to write to NTFS partitions should prevent you from mounting an hibernated partition as said in its manual:
remove_hiberfile
Unlike in case of read-only mount, the read-write mount is
denied if the NTFS volume is hibernated. One needs either to
resume Windows and shutdown it properly, or use this option which will
remove the Windows hibernation file. Please note, this means that the
saved Windows session will be completely lost. Use this option under
your own responsibility.
And also has an option for read-only in this case:
ro
Mount filesystem read-only. Useful if Windows is hibernated or
the NTFS journal file is unclean.