System Details:

python 3.5.1
pytest 3.0.2
pytest-cov 2.3.1
PyCharm Community Edition 2016.2.2
Build #PC-162.1812.1, built on August 16, 2016
JRE: 1.8.0_76-release-b216 x86
JVM: OpenJDK Server VM by JetBrains s.r.o

MCVE:

main.py

def foo():
    x = 10
    return x

test.py

import main

def test_foo():
    assert main.foo() == 10

Create a new project in PyCharm with those two files and create a new test config with the following options --cov=. --cov-report term-missing -rw -vv. Set a breakpoint on any line of code and hit debug.

Expected result:
The breakpoints work.

Actual result:
The breakpoints don't work.

If you remove the options, it hits the breakpoints fine.