На одной ноде: , e.what() = DB::Exception (from IP:35464) (in query:

OPTIMIZE TABLE event2 PARTITION 201811 FINAL), Stack trace:

0. /usr/bin/clickhouse-server(StackTrace::StackTrace()+0x16) [0x56d06c6]
1. /usr/bin/clickhouse-server(DB::readException(DB::Exception&, DB::ReadBuffer&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xc1e) [0x56f596e]
2. /usr/bin/clickhouse-server(DB::Connection::receiveException()+0x81) [0x5110f01]
3. /usr/bin/clickhouse-server(DB::Connection::receiveHello()+0x1b8) [0x5111468]
4. /usr/bin/clickhouse-server(DB::Connection::connect()+0x222) [0x5113672]
5. /usr/bin/clickhouse-server(DB::Connection::sendQuery(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, DB::Settings const*, DB::ClientInfo const*, bool)+0x11d5) [0x5116ae5]
6. /usr/bin/clickhouse-server(DB::MultiplexedConnections::sendQuery(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, DB::ClientInfo const*, bool)+0xdc) [0x512430c]
7. /usr/bin/clickhouse-server(DB::RemoteBlockInputStream::sendQuery()+0x30c) [0x4777e2c]
8. /usr/bin/clickhouse-server(DB::copyData(DB::IBlockInputStream&, DB::IBlockOutputStream&, std::atomic<bool>*)+0x36) [0x477e776]
9. /usr/bin/clickhouse-server(DB::StorageReplicatedMergeTree::sendRequestToLeaderReplica(std::shared_ptr<DB::IAST> const&, DB::Settings const&)+0xac3) [0x4ffab73]
10. /usr/bin/clickhouse-server(DB::StorageReplicatedMergeTree::optimize(std::shared_ptr<DB::IAST> const&, std::shared_ptr<DB::IAST> const&, bool, bool, DB::Context const&)+0x3f2) [0x4ffb682]
11. /usr/bin/clickhouse-server(DB::InterpreterOptimizeQuery::execute()+0x391) [0x4e6e011]
12. /usr/bin/clickhouse-server() [0x4ef544b]
13. /usr/bin/clickhouse-server(DB::executeQuery(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, DB::Context&, bool, DB::QueryProcessingStage::Enum)+0x8a) [0x4ef646a]
14. /usr/bin/clickhouse-server(DB::TCPHandler::runImpl()+0x3d7) [0x2daf907]
15. /usr/bin/clickhouse-server(DB::TCPHandler::run()+0x2b) [0x2db07ab]
16. /usr/bin/clickhouse-server(Poco::Net::TCPServerConnection::start()+0xf) [0x58c510f]
17. /usr/bin/clickhouse-server(Poco::Net::TCPServerDispatcher::run()+0x16a) [0x58c54ea]
18. /usr/bin/clickhouse-server(Poco::PooledThread::run()+0x77) [0x59668f7]
19. /usr/bin/clickhouse-server(Poco::ThreadImpl::runnableEntry(void*)+0x38) [0x59627b8]
20. /usr/bin/clickhouse-server() [0x930310f]
21. /lib/x86_64-linux-gnu/libpthread.so.0(+0x76db) [0x7fe36fafc6db]
22. /lib/x86_64-linux-gnu/libc.so.6(clone+0x3f) [0x7fe36f28388f]

На другой ноде:
2018.11.30 16:33:10.607250 [ 10764 ] <Debug> executeQuery: (from IP:36696, query_id: f0aa5c17-37b4-4b56-9ef3-2516dd348208) OPTIMIZE TABLE event2 PARTITION 201811 FINAL
2018.11.30 16:33:10.608785 [ 10764 ] <Information> event2 (StorageReplicatedMergeTree): Cannot select parts for optimization: Part 20181102_20181129_3508_4242_4 has already been assigned a merge into 20181102_20181129_3508_7254_5


Мне не очень очевидно из логов, проблема в размере партиции?..

Ну вроде бы у вас уже назначился какой-то мерж. Он, наверное, в процессе выполнения. Что-нибудь есть в system.merges ?