Fix

src/main/java/org/telegram/telegrambots/api/methods/updates/GetUpdates.java

@@ -31,7 +31,8 @@ public class GetUpdates implements IToJson {
      */
     private Integer limit;
     /**
-     * Optional	Timeout in seconds for long polling. Defaults to 0, i.e. usual short polling
+     * Optional. Timeout in seconds for long polling. Defaults to 0, i.e. usual short polling.
+     * Should be positive, 0 should be used for testing purposes only.
      */
     private Integer timeout;
 

src/main/java/org/telegram/telegrambots/api/objects/CallbackQuery.java

@@ -19,6 +19,10 @@ import java.io.IOException;
  * the field message will be present. If the button was attached to a message sent via the bot
  * (in inline mode), the field inline_message_id will be present.
  * @note Exactly one of the fields data or game_short_name will be present.
+ * @note  After the user presses an inline button, Telegram clients will display a progress bar
+ * until you call answerCallbackQuery. It is, therefore, necessary to react by
+ * calling answerCallbackQuery even if no notification to the user is needed
+ * (e.g., without specifying any of the optional parameters).
  * @date 10 of April of 2016
  */
 public class CallbackQuery implements IBotApiObject {

src/main/java/org/telegram/telegrambots/updatesreceivers/BotSession.java

@@ -149,7 +149,9 @@ public class BotSession {
                         BotLogger.severe(LOGTAG, e);
                     }
                 } catch (InterruptedException e) {
+                    if (!running) {
                         receivedUpdates.clear();
+                    }
                     BotLogger.debug(LOGTAG, e);
                 } catch (Exception global) {
                     BotLogger.severe(LOGTAG, global);
@@ -158,7 +160,9 @@ public class BotSession {
                             this.wait(500);
                         }
                     } catch (InterruptedException e) {
+                        if (!running) {
                             receivedUpdates.clear();
+                        }
                         BotLogger.debug(LOGTAG, e);
                     }
                 }