Code coverage measurement is an important element in white-box testing, both in industrial practice and academic research. Other related areas are highly dependent on code coverage as well, including test case generation, test prioritization, fault localization, and others. Inaccuracies of a code coverage tool sometimes do not matter that much but in certain situations they can lead to serious confusion. For Java, the prevalent approach to code coverage measurement is to use bytecode instrumentation due to its various benefits over source code instrumentation. However, if the results are to be mapped back to source code this may lead to inaccuracies due to the differences between the two program representations. In this paper, we systematically investigate the amount of differences in the results of these two Java code coverage approaches, enumerate the possible reasons and discuss the implications on various applications. For this purpose, we relied on two widely used tools to represent the two approaches and a set of benchmark programs from the open source domain.