The bug seems to be triggered when there is a print with end='' followed by a print that begins with a \n.

Minimal example:

$ bpython3
bpython version 0.17.1 on top of Python 3.6.6 /usr/bin/python3
>>> print('foo', end=''); print('\nbar')
foo

bar
>>>

Expected: foo and bar are in immediately adjacent lines.
Actual: There is an extraneous line between foo and bar.

For reference, observe what the standard python interpreter does:

$ python3
Python 3.6.6 (default, Jun 27 2018, 14:44:17) 
[GCC 8.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> print('foo', end=''); print('\nbar')
foo
bar
>>> 

I have the hunch that the bug probably lives in the stdio shim of bpython. The bugtracker shows no similar bugs.