When doing out-of-tree builds it's not expected that the build (or tests) clutter the source path. All build output should be written to the build path (the current directory when configure is run) and subdirectories of that.
(theoretically it should even be possible to have the source on a read-only mount, but that's not really important imo, the point is to not clutter the git repository with build output)
However, after running make check there will be a while slew of *.log files in the source directory:
bitcoin$ ./autogen.sh
bitcoin$ make build
bitcoin$ cd build
bitcoin/build$ ../configure ...
bitcoin/build$ make check
bitcoin/build$ cd ..
bitcoin$ ls src/test/*.log
src/test/addrman_tests.cpp.log src/test/compress_tests.cpp.log src/test/netbase_tests.cpp.log src/test/sigopcount_tests.cpp.log
src/test/allocator_tests.cpp.log src/test/crypto_tests.cpp.log src/test/net_tests.cpp.log src/test/skiplist_tests.cpp.log
src/test/amount_tests.cpp.log src/test/cuckoocache_tests.cpp.log src/test/pmt_tests.cpp.log src/test/streams_tests.cpp.log
src/test/arith_uint256_tests.cpp.log src/test/dbwrapper_tests.cpp.log src/test/policyestimator_tests.cpp.log src/test/sync_tests.cpp.log
...
Either these files should be written to a temporary path (like the other test output), or to the build directory.